One motion called for the company to abandon nuclear energy in the wake of the Fukushima Daiichi nuclear crisis, although this was defeated.
Tepco may have to pay compensation of almost $100bn (?63bn) following radiation leaks at its nuclear plant.
Tepco shares have plunged 85% since the tsunami damaged the Fukushima plant.
The disaster caused a meltdown at three of the six reactors, and more than three months on radioactive material continues to leak from the facility.
Shareholders have criticised Tepco's management for their slow response to the crisis, accusing them of putting out inaccurate data and displaying a lack of transparency.
Some 80,000 residents living close to the plant have been forced to abandon their properties.
Executives at the meeting in Tokyo issued an apology amid angry shouts and heckling by shareholders.
One shareholder said the senior executives should commit suicide by jumping into the damaged reactors.
"All of us directors apologise deeply for the troubles and fears that the accident has caused. We're working to resolve this crisis as quickly as possible," said Tepco chairman Tsunehisa Katsumata.
Tepco has said it hoped to achieve a cold shutdown of the plant by January next year.
Earthquake riskThe biggest debate among shareholders revolved around the future of nuclear energy and what the company's stand on the issue should be.
Opponents failed to win enough support for a motion that would have forced Tepco to scrap all reactors and halt any construction of new ones.They said nuclear power did not have a feasible future, not least because of the ongoing Fukushima nuclear crisis.
"Japan has a lot of earthquakes and after this accident I just don't think there is such a thing as safe nuclear power here," said one shareholder, Takako Kameoka.
Japan relies on nuclear power for 30% of its electricity needs.
Although thousands of those present at the six-hour meeting supported the motion, the institutional shareholders that own most of the stock were not swayed, and the motion was defeated.
Analysts said that the current power shortage in Japan was proof that the country needed nuclear power in order to meet its energy demands.
"The question is, can Japan do without nuclear power?" said Mitsushige Akino, of Ichiyoshi Investment Management Company.
"How much are the Japanese people willing to sacrifice in terms of standard of living? The sentiment is understandable, but the reality is that this is difficult without considerable sacrifice to economic growth and activity."
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