AFP Commissioner Mick Keelty says the referral was made on February 23 and came by way of federal Justice Minister Chris Ellison.
He said investigations were ongoing but Mr Keelty wanted to make it clear that no government minister was under investigation.
"I can confirm the receipt of referrals for investigation from the Department of Foreign Affairs and Trade in relation to certain Australian companies in alleged breaches of trade sanctions," he told a Senate estimates committee hearing.
"These are matters that fall outside the Cole inquiry's terms of reference.
"I can confirm that one of the alleged breaches of trade sanctions related to an Australian company importing oil into Australia."
Mr Keelty said in addition to that case, there were six others, although not all were to do with oil.
"They are breaches of the oil-for-food sanctions. They are not all to do with an oil company. Some of them, as I recall, are to do with chemicals and other commercial type of activities," he said.
Mr Keelty said investigations were continuing and he could provide no further comment because it may lead to the companies knowing they were being investigated.
Mr Keelty said the investigation of the one importation issue related to the actions of the company.
"Whether that translates to actions of individuals will no doubt come to light as the investigation continues," he said.
Foreign Minister Alexander Downer confirmed that the AFP was investigating companies who may have breached UN sanctions, after Labor frontbencher Kelvin Thomson asked what Mr Downer had done to ensure that there had been no breach of UN sanctions in October 2000 when the Iraqi vessel Poul Spirit berthed in Fremantle in Western Australia and discharged 90 million litres of oil.
Wheat scandal
Mr Keelty’s revelations come as the Cole inquiry, which investigated $290 million in kickbacks paid by wheat exporter AWB to Saddam Hussein’s regime, prepares its final report.
That report is expected to be finished, and handed to relevant government ministers, by November 24.
Senator Ellison said the Cole commission emerged from the UN Volcker inquiry into rorting of the UN oil-for-food program.
"Any other matters extraneous to that can be adequately dealt with by AFP investigation," he said.
Senator Ellison rejected suggestions that the government should consider amending the Cole Inquiry’s terms of reference to allow it to investigate.
He said that to deal with the new allegations by way of the inquiry would involve a much slower path.