The leaks renewed fears over safety in Japan's nuclear industry, whose image has been tarnished by scandals over cover-ups and fudged safety records.
About 1,200 litres of radioactive water also leaked into the sea from a reactor at the world's biggest nuclear plant in terms of power output capacity, and a fire erupted in an electricity transformer.
Tsunehisa Katsumata, Tepco's president, apologised to Hiroshi Aida, mayor of nearby Kashiwazaki, the city worst hit in the tremor.
"I apologise for causing you worry and trouble," he said.
Katsumata toured the plant on Wednesday morning, declaring it "a mess".
"I think we can say the size of the earthquake was beyond our expectations," he said.
|The quake forced thousands of people |
to flee to evacuation centres [EPA]
"We will conduct an investigation from the ground up. But I think fundamentally we have confirmed that our safety measures worked," he said, adding that "it is hard to make everything go perfectly".
The company said reactors closed down automatically in the quake and all emissions were well within government safety guidelines, presenting no threat to the environment, but local people voiced unease.
"We've had two big ones in three years," said 60-year-old Hoshi Murofushi, who was sheltering with her two grandchildren in an evacuation centre in Kariwa.
"There's no guarantee that there won't be another one. It will be too late if we have another Chernobyl," she said.
Aida order that the plan not be re-started until safety could be ensured.
Nine elderly people died and more than 1,100 were injured in the quake.
It flattened hundreds of homes, and thousands of people are staying in evacuation centres.
Senior officials including Shinzo Abe, the prime minister, criticised Tepco for being slow to issue information, saying it risked undermining public trust in the nuclear industry.
Yasuhisa Shiozaki, the chief cabinet secretary, urged Tepco to be more transparent in reporting problems, especially those that may impact the public.
"We want the report itself to be honest and we want it quickly," he said.
But he added that it was important not to cause unnecessary concern.
Quake proofing regulations for nuclear power stations were stepped up last year, requiring power companies to re-assess the risks for their reactors.