Iran has allowed Nigeria to interview an Iranian citizen inside its embassy, in connection with a shipment of arms seized in Lagos.
Iran was accused of being behind the arms and there were suggestions Nigeria was being used as a smuggling route.
But security sources say Iran has pledged to co-operate fully with the investigation.
Nigeria has said it will report Iran to the UN if investigations showed UN sanctions had been broken.
Iran is under sanctions because of its nuclear programme.
Iran's Foreign Minister Manouchehr Mottaki has travelled to Nigeria to discuss the issue with his Nigerian counterpart, Odein Ajumogobia, who told the BBC both countries would prefer to clear the air over the incident.
Mr Ajumogobia said Mr Mottaki had promised to co-operate with the investigations and had given Nigerian authorities access to a suspect in the Iranian embassy.
Nigeria also wants to question another Iranian inside the embassy but has been unable to do so as he has diplomatic immunity.
"If the Iranians are willing to waive immunity, then we will pursue that," Mr Ajumogobia said.
Nigeria's authorities have described discovering an arsenal in Lagos two weeks ago, which included rocket launchers, grenades and mortars.
Mr Ajumogobia told reporters that investigations had shown that the weapons did indeed come from Iran.
"That's been confirmed from our own shipping documents and the Iranian foreign minister," he said.
But he said there was no indication that the shipment had broken the UN sanctions as no nuclear materials had been involved.
"If Nigeria finds in the conclusion of investigations that there has been a breach of any sanctions, as a member of the UN Council we would do what is necessary," he said.
It was initially feared that the weapons could be used in Nigeria - by oil militants in the Niger Delta, or Islamist radicals in the north or in elections due next year.
But the BBC's Caroline Duffield in Lagos says security sources now believe Nigeria's port may have been targeted as a holding destination - thanks to the country's reputation for corruption and lax regulations.
The idea that Nigeria might be being used as an arms-smuggling route clearly has angered the government, says our correspondent.
The France-based shipping company CMA CGM says there were attempts to send the containers on - to The Gambia, in West Africa - before the Nigerian police seized them.
It says the shipment came from Bandar Abbas, a port in southern Iran, and were hidden in containers labelled as building materials.
Two people who handled the shipment have been arrested.