Yukiya Amano said UN experts should be able to carry out random reviews of nuclear power stations.
He has also called for countries to carry out risk assessments on their reactors within 18 months.
The watchdog, the IAEA, is holding a meeting in Vienna aimed at improving nuclear safety.
Officials from 150 nations are meeting at the International Atomic Energy Agency (IAEA) offices in Vienna.
Mr Amano said nations had to respond to the great public anxiety caused by the Fukushima accident.
"Public confidence in the safety of nuclear power has been badly shaken. However, nuclear power will remain important for many countries, so it is imperative that the most stringent safety measures and implemented everywhere," he said.
He also wants UN experts to be permitted to perform random safety reviews of their reactors.
The suggestion that UN experts perform random checks is controversial, says the BBC's Bethany Bell in Vienna.
At the moment, there are no compulsory international nuclear safety regulations as many countries believe nuclear safety is the responsibility of individual states.
'Unprecedented emergency'The Fukushima disaster has prompted widespread public concern about nuclear safety.
The nuclear plant's cooling systems were knocked out by the 11 March earthquake and tsunami. The disaster caused meltdown at three of the reactors.
Continue reading the main story Reactor 1: Partial meltdown from cooling problems. Building holed by gas explosion. Radioactive water detected in reactor and basementReactor 2: Partial meltdown from cooling problems. Building holed by gas blast; containment damage suspected. Highly radioactive water detected in reactor and adjoining tunnelReactor 3: Partial meltdown from cooling problems. Building holed by gas blast; containment damage possible. Spent fuel pond partly refilled with water after running low. Radioactive water detected in reactor and basementReactor 4: Reactor shut down prior to quake. Fires and explosion in spent fuel pond; water level partly restoredReactors 5 & 6: Reactors shut down. Temperature of spent fuel pools now lowered after rising highMore than three months after the accident, the facility is still leaking radioactive material.Germany has decided to shut down all its reactors by 2022 and Italy has voted against plans to revive nuclear power.
The IAEA report on the Fukushima accident is to be published on Monday at the conference.
Leaks from the report indicate it has found that Japan did not follow all the proper guidelines for how to respond to the crisis.
It failed to follow some safety measures, and did not learn from past threats to nuclear plants in areas prone to tsunami risk, according to leaks.
But it will also praise the dangerous and hard work carried out by Japan's nuclear workers.
"The operators were faced with a catastrophic, unprecedented emergency scenario with no power, reactor control or instrumentation," the 160-page report will say.
Some 110,000 tonnes of water have built up during efforts to cool reactors since the twin natural disasters, hampering work to bring the plant under control.
The contaminated water, enough to fill 40 Olympic-sized swimming pools, is increasing by 500 tonnes a day as fresh water is continuously being injected to cool the reactors.
An operation on Friday to decontaminate the water was abandoned after just a few hours because of a rapid rise in radiation.
Japanese broadcaster NHK reported that storage facilities are filling up, so a delay in restarting the filtering system could cause the water to overflow into the sea in about a week.
Fukushima is the world's worst nuclear accident since Chernobyl in Ukraine in 1986.
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