In separate meetings with Prime Minister Junichiro Koizumi and Foreign Minister Yoriko Kawaguchi, Kharazi said Iran was willing to agree to a tougher 'additional protocols' inspection regime by the International Atomic Energy Agency (IAEA), the official said.
"We have made this decision under fierce opposition domestically," Kharazi was quoted as telling Koizumi by the official.
"It was a problem that we did not report some (nuclear) activities, but they were not for military purposes," Kharazi said.
Iran's diplomatic plea came less than a week before the IAEA's board of governors is to meet to consider whether Tehran's nuclear program should be referred to the UN Security Council, which could impose punitive sanctions.
On November 20 the IAEA board will study a report from its director general, Mohamed ElBaradei, that accuses Iran of covert nuclear activities over the past 20 years, including producing plutonium and enriching uranium.
But the report says there is as yet no evidence Tehran is trying to produce a nuclear bomb, according to a copy obtained by AFP.
"We ask for your cooperation at the November (IAEA) meeting, so it will be not referred to the US Security Council," Kharazi told Koizumi, according to the official.
He added activities were covered up to avoid punishment by the United Nations, the official said.
Koizumi praised Iran's efforts over the past month, which have included providing a full report on its nuclear activities and admitting to violations of nuclear safeguards agreements, and urged further work.