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Shih Yen-hsiang told parliament that the three nuclear power plants, owned and operated by the state-run Taiwan Power Co (Taipower), were safe but the government was ready to enhance their safety.
"As the public has become increasingly concerned about the safety issues of the local nuclear power plants, the economic ministry has decided to raise the safety standards of the plants," he said.
Shih pledged to give priority to safety over money.
At the ministry's order, Taipower plans to come up with an initial evaluation report on its atomic energy facilities next month, which will be used as a reference to company enhance their safety standards.
Shih had said the government was unlikely to scrap the three plants or halt building a new atomic facility, which is half-completed, as the island is heavily reliant on energy imports.
Electricity generated by the three nuclear plants accounts for 20 per cent of Taiwan's power supply.
Concerns about the island's atomic plants have been mounting after a 9.0-magnitude earthquake and ensuing tsunami struck Japan on March 11, crippling a nuclear power plant in Fukushima.
Around 2,000 anti-nuclear protesters took to Taipei's streets in March and campaigners plan to mobilise tens of thousands of demonstrators at a rally on April 30.
Taiwan is regularly hit by earthquakes as the island lies near the junction of two tectonic plates.
In September 1999, a 7.6-magnitude tremor killed around 2,400 people in the deadliest natural disaster in the island's recent history.
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