"We welcome... the IAEA's resolution. Iran must take it seriously," said Chief Cabinet Secretary Yasuo Fukuda.
"We hope Iran will sincerely fulfill the requirements of the IAEA resolution."
On Saturday the UN nuclear watchdog adopted a US-backed resolution condemning Iran for hiding possibly weapons-related nuclear activities, drawing ire from Tehran, which suspended inspections.
The United States wants to send the issue of Iran secretly developing nuclear weapons to the UN Security Council, a move that could result in sanctions against Tehran.
Japan last month signed a two-billion-dollar deal with Iran to develop the massive Azadegan oilfield in order to ensure stable oil supplies despite the United States expressing "deep concern" over the deal.
A Japanese foreign ministry official said it was in Japan's interests to call on Iran to solve its nuclear question as Tehran's attitude would eventually affect Japanese energy policy.
"We hope there won't be sanctions against Iran. So that's why we are urging Iran to solve the problem," he said.
"I suppose it is not impossible that the United Nations will impose sanctions against Iran. We do not want that. We hope Iran would respond appropriately," he said.
Various Japanese officials have said Tokyo regards the nuclear and oil issues as separate.
Foreign Minister Yoriko Kawaguchi made clear last year that Iran's dealings with the IAEA on nuclear non-proliferation would not hinder talks on the oil deal which were still under way at the time.
At the time Kawaguchi described securing oil supplies as "a very important policy goal for Japan."