In a statement from his spokesman, Annan said he "encourages the IAEA (International Atomic Energy Agency), the government of Iran and the other governments that have been working with Iran...to continue their efforts."
He also welcomed Iran's announcement that it has stopped enriching nuclear materials, the spokesman said.
Iran is trying to keep its nuclear programme from being taken up by the UN Security Council, which could impose punitive sanctions on Tehran.
The IAEA board meets next week in Vienna to consider the agency's report on Iran and if it finds the country in violation of the nuclear Non-Proliferation Treaty, it could refer the matter to the council.
The report was the result of eight months of investigations, including dozens of trips by inspectors to Iran and intensive laboratory analyses of samples, since IAEA director-general Mohammed ElBaradei visited Iran to check out reports of undeclared nuclear facilities.
In it, ElBaradei accuses Iran of covert nuclear activities over the past 20 years, including producing plutonium and enriching uranium, but says there is not yet evidence Tehran is trying to produce an atomic weapon.
The United States accuses the Islamic republic of trying to build an atomic weapon and called the report "impossible to believe."