Iranian Foreign Minister Ali Akbar Salehi is in Nigeria for a meeting of eight developing countries that want to boost trade, government officials and diplomats said Thursday.
Relations between Iran and Nigeria got frosty last year following the discovery in Lagos of a weapons shipment that was loaded in Iran.
"He came to Nigeria for a D8 meeting of ministers and commissioners," Nigeria's foreign affairs spokesman Damian Agwu told AFP.
Iranian embassy officials also confirmed the minister's visit.
An alleged Iranian Revolutionary Guard member is on trial over the importation of rockets, explosives and grenades falsely declared as building materials. The arms were seized in October at Nigeria's main port in the economic hub of Lagos.
The case drew international attention because it may constitute a violation of UN sanctions against Iran over its nuclear programme.
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Nigeria reported the seizure to the UN Security Council, which has approved four sets of sanctions against Iran, including a ban on arms sales.
Agwu said the visit had nothing to do with the arms case.
"It's far from that. There was no connection. He came specifically for the D8 meeting."
Nigeria currently holds the rotating chairmanship of the Istanbul-based D8 group. It is the only non-Muslim nation in the group which comprise Bangladesh, Egypt, Indonesia, Iran, Malaysia, Nigeria, Pakistan and Turkey, with a total population of 930 million people.
Muslims make up an estimated half of Nigeria's 150 million population.
One of the major goals of the body is to create a free-trade zone.
The deputy prime minister of Turkey, Bulent Arinc, also attended the three-day meeting which started on Tuesday.