The decision is not which port is better. It is which port is cheaper for this box, this destination, this quarter.
Two Lagos ports. One 40-foot standard container. The terminal bill at Lekki is published and itemised. The Apapa terminal bill is not, in any form I could retrieve from the operator or the Nigerian Ports Authority. The haulage figures circulating for both ports are secondary, directional, and move between bookings. That asymmetry is the story: you can build a landed-cost worksheet, but you cannot outsource the verdict to a rate card that does not exist.
What follows is a worksheet, not a ranking. It separates the line items you can verify from the ones you have to quote yourself, and it shows where the swing actually lives.
What Lekki’s published tariff actually says
Lekki Freeport Terminal publishes a cargo-owner tariff with an effective date of 16 February 2026. For a 40-foot standard import, the terminal handling charge is ₦300,056.40. The delivery charge is ₦18,152.00. Both are naira-denominated and both sit inside the terminal bill, before customs duty, before haulage, before anything moves.
The same schedule lists optional charges that matter more than importers expect. A 40-foot customs exam charge is ₦104,611.50. A 40-foot scanning charge is ₦104,611.50. Fast-track is ₦35,721.00 for a 40-foot. Repositioning a 40-foot container is ₦104,611.50. These are not automatic, but they are not rare either, and they are large enough to change the arithmetic on a single box.
The tariff also states that VAT applies to all charges per Nigerian VAT laws, and that tariffs may be modified at any time subject to economic conditions and market prices, with prior notification. Read that as: the published number is a baseline, not a guarantee.
The storage clock is part of the landed cost
Lekki’s import storage is free for the first five days for standard containers. From day six to eight, a 40-foot standard is charged ₦13,200. From day nine to thirteen, ₦64,680. From day fourteen onwards, ₦88,200. The tiers are steep and they are daily.
This is where a slow customs clearance turns a terminal-bill advantage into a loss. A box that clears in four days pays nothing in storage. A box that clears in fifteen days pays ₦88,200 per day from day fourteen, on top of handling, delivery, and any exam or scanning charges. The port decision is partly a clearance-timeline decision, and the clearance timeline is not published by either port in a form you can rely on for planning.
What the tariff does not include
The Lekki tariff covers the terminal. It does not cover haulage from the terminal gate to your warehouse, your factory, or your customer in Ibadan, Abeokuta, or Kano. It does not cover corridor delays, informal payments, or the cost of a truck sitting idle because a slot did not open.
The Nigerian Ports Authority tariff page describes the regulatory framework, definitions, and the rule that naira-denominated rates are adjusted triennially against the Nigeria CPI-U average of the previous three years. It does not, in the retrieved text, give a comparable Apapa 40-foot terminal handling figure. That gap is not a research failure on your part. It is the state of published information.
The haulage variable, labelled honestly
The only retrieved directional data point on haulage comes from a secondary logistics source, Glottis, which reports 40-foot haulage costs of ₦900,000 at Apapa, ₦350,000 at Tin Can Island, and ₦550,000 at Lekki. Treat that as a hypothesis, not a rate. It is a single source with no stated methodology and no date attached to the figures in the retrieved excerpt.
A LinkedIn post by a logistics commentator, Olukunle Fashina, offers a different directional picture: Apapa haulage dropped to roughly ₦350,000 in 2025 after checkpoint reform, then crept back past ₦360,000 plus up to ₦80,000 in informal tolls by mid-2026 as gridlock returned. Lekki held closer to ₦550,000, with no comparable toll exposure but a longer average haul to inland markets. The same post states that for a container headed to Ibadan, Apapa still came out about ₦110,000 cheaper, tolls included, and that the result could flip within a quarter.
Both sources are secondary. Neither is an audited rate card. The honest use of them is to set a range for your own quotes, not to conclude which port wins.
The worksheet
For each shipment, build four lines per port:
- Terminal bill. For Lekki, start from ₦300,056.40 handling plus ₦18,152.00 delivery, then add any exam, scanning, fast-track, or repositioning charge that applies to your box. For Apapa, get the terminal operator’s current schedule in writing; do not substitute a number from a blog.
- Haulage to the actual destination. Not to “Lagos.” To the specific warehouse, factory, or customer address. Get two written quotes per port per destination. The spread between quotes is often larger than the spread between ports.
- Expected corridor delay cost. If your haulier prices waiting time separately, or if informal payments are a known feature of the route, put a number against it. If you cannot, at least record the assumption so you can revise it next quarter.
- Storage exposure. Estimate your clearance days. If the estimate runs past five days at Lekki, add the tiered storage charge. If it runs past fourteen, add ₦88,200 per day for a 40-foot standard.
The port choice falls out of the sum. It does not fall out of reputation, and it does not fall out of a single published tariff.
A worked example, clearly hypothetical
Assume a 40-foot standard container of general merchandise, destination a warehouse in Ibadan, clearance estimated at seven days, no exam or scanning triggered.
Lekki: handling ₦300,056.40 + delivery ₦18,152.00 + storage for days six and seven (2 × ₦13,200 = ₦26,400) + haulage quote of ₦550,000 = ₦894,608.40 before VAT and before duty.
Apapa: terminal handling figure from your operator’s written schedule (substitute your own) + haulage quote of ₦360,000 + informal toll allowance of ₦80,000 + corridor delay allowance (substitute your own) = the Apapa column.
The example is not a finding. It is a template. The numbers you substitute are the ones that matter, and they will differ from mine, from Glottis’s, and from Fashina’s.
Why the answer moves between bookings
Neither port publishes an audited all-in rate card. Fashina’s post says this directly: “which is cheaper” is a question you have to re-ask every time you book. That is not a rhetorical flourish. It is the operational reality of a corridor where haulage rates respond to checkpoint policy, gridlock, and fuel costs within a quarter, and where terminal tariffs are explicitly subject to modification with prior notification.
The practical rule: get two written haulage quotes per port per destination before every booking, confirm the terminal operator’s current schedule in writing, and record your clearance-day estimate so you can compare it against what actually happened. Over three or four shipments, your own data becomes more useful than any published comparison.
The decision class
This is a siting and logistics-mix decision crossed with a timing decision. It is not a permanent port loyalty choice. A Lagos Island consignee and an Ibadan consignee can have different right answers on the same day. The same consignee can have a different right answer next quarter. The worksheet is the durable asset; the verdict is perishable.
Lekki’s published tariff is unusually useful because it is itemised. It lets you separate the fixed terminal component from the variable haulage and delay components, which is where the real swing lives. Apapa’s advantage, where it exists, is in the haulage leg for certain inland destinations, and that advantage is contingent on corridor conditions that are not published and not stable.
Build the worksheet. Quote both legs. Re-run it every booking. That is the whole method.
FAQ
Is Lekki cheaper than Apapa for a 40-foot container?
Not necessarily, and not permanently. Lekki’s terminal bill is published and itemised; Apapa’s comparable terminal figure is not in the retrieved sources. The haulage figures circulating are secondary and directional. The all-in answer depends on your destination, your clearance timeline, and the quotes you get for that specific booking.
What is Lekki’s terminal handling charge for a 40-foot standard import?
₦300,056.40, per the Lekki Freeport Terminal tariff effective 16 February 2026. Delivery is ₦18,152.00. VAT applies to all charges per Nigerian VAT laws.
How long is Lekki’s free storage window?
Five days for standard import containers. From day six to eight, a 40-foot standard is charged ₦13,200; from day nine to thirteen, ₦64,680; from day fourteen onwards, ₦88,200 per day.
Does the Lekki tariff include haulage?
No. It covers terminal handling, delivery, and listed additional charges. Haulage from the terminal gate to your destination is a separate cost and must be quoted separately.
Why can’t I find a published Apapa 40-foot terminal handling charge?
The retrieved sources do not contain a comparable published figure from the Apapa terminal operator or the Nigerian Ports Authority. The NPA tariff page describes the regulatory framework and definitions but does not, in the retrieved text, give a 40-foot Apapa terminal handling number. Ask the terminal operator for the current schedule in writing.
Should I switch ports every quarter?
Switch when the worksheet says the sum is lower, not on reputation or a single published comparison. The right answer for a Lagos Island consignee and an Ibadan consignee can differ, and the right answer for the same consignee can change between quarters.