A Nigerian court on Monday sentenced an alleged member of the Iranian Revolutionary Guard and his Nigerian accomplice to five years in jail each over an illegal arms shipment.

Azim Aghajani and Nigerian Ali Abbas Jega were detained in 2010 when authorities at a Lagos port discovered 13 containers of weapons that had been declared as construction materials.

The case attracted wide international attention, in part because it raised questions over whether Iran had violated United Nations sanctions on weapons sales.

West African governments also warned that Iran may have been seeking to send weapons to rebel groups in the region.

Federal High Court Judge Okechukwu Okeke pronounced the two "guilty as charged" on four of five criminal counts, with the sentences for each count to be served concurrently.

While the crimes in question carried a potential life sentence, the judge said he was swayed by a plea for leniency from the defence and by the conduct of the pair while in detention.

"In sentencing the accused I have taken into consideration the plea for mercy by the defence team, but the law has to take its course," Okeke said.

The sentence will be counted retroactively from February 2011, when their trial began, meaning the men will walk free in under three years.

Jiti Ogunye, a Lagos-based lawyer and commentator who followed the case, told AFP he was "shocked" by the light jail terms, especially by the decision to have the sentences served concurrently.

"Given how the case was going and the avalanche of evidence...everybody was expecting a conviction with a heavy sentence," Ogunye said.

"It shows there is something very, very wrong with our criminal justice system," he continued.

"When a verdict in any case falls short of the expected outcome, there are bound to be worries...that something improper might have happened," he said.

He explained that Nigeria's judiciary has long been plagued by systemic problems, including corruption and political pressures heavily influencing verdicts, but he could not comment directly on the Iranian case before reviewing the decision.

Aghajani has denied having links with Iran's powerful Revolutionary Guard, insisting he was a private businessman conducting a legitimate transaction.

The defence argued that the weapons were just passing through Nigeria and were ultimately headed to the tiny nation of Gambia as part of a legal sale.

Gambia denied it was the intended recipient and cut diplomatic ties with Iran over the dispute.

The case also sparked a stern response from Senegal, which accused Iran of trying to deliver weapons to separatist rebels in its southern Casamance region.

The United Nations added Aghajani to a blacklist last year, labelling him a Revolutionary Guard member tied to "Iranian support for terrorism and extremism worldwide".

The United States has also put Aghajani on its national sanctions list.

Addressing the court before his sentence was read out, the Iranian described his time in Nigerian jails as "agony".

"It has been a very sad experience for me for three years," he said.

Judge Okeke denied a request by Aghajani's lawyer for the sentence to be served in Iran.

Jega claimed he was told the cargo contained construction materials and said he was hired by the Iranian as a middle-man to help clear the shipment through the Nigerian port.

"I did not know what was there were arms. If I had known I would not have waited to be arrested by the police," he said on Monday before sentencing. "I ask for leniency."

The arms, which include heavy weaponry, are to be given to the Nigerian government, the court ruled.