The death toll from Typhoon Morakot was raised to at least 650 on Sunday after the worst weather disaster to hit Taiwan in half a century.
Premier Liu Chao-shiuan said 160 were confirmed killed, with another 490 listed as missing and presumed dead. DNA tests will be conducted on battered bodies that authorities have not yet been able to identify, Liu said.
The storm that hit two weeks ago triggered landslides and widespread flooding that trapped thousands of people in remote southern villages for days.
Television footage on Sunday showed soldiers and students scrubbing homes and streets in the southern city of Linbien in Pingtung county, which was still flooded in knee-deep waters because drainage ditches were blocked by debris.
Hundreds of soldiers in camouflage also waded through floodwaters to the area where homes once stood in Shiao Lin, the village hardest-hit by massive mudslides.
Some were searching for floating bodies. Others were preparing to dig up the more than 400 bodies believed buried under several metres of mud, said military relief operation spokesman Tai Chan-teh.
Dozens of surviving Shiao Lin residents have demanded the government investigate the cause of the landslides that wiped out their village.
Many blame the deluge on a government project that used explosives on several mountains to blast open an area for a water pipe to funnel water from the Laonung River into a reservoir. They say part of the mountain collapsed after two days of torrential rain.
Officials say the project had been carefully assessed to avoid environmental damage.
The government’s slow rescue operation has led to villagers accusing officials of failing to act promptly and critics blaming authorities for failing to order evacuations.
President Ma-Ying-jeou has struggled to calm widespread anger as his approval rating has plunged to below 20 per cent.
Ma has been visiting hard-hit areas in the south over the past few days and promising that a planned $US3 billion ($A3.61 billion) reconstruction program will be carried out with exemplary efficiency.
He has promised a Cabinet reshuffle by early September but has rejected widespread demands to replace Premier Liu, who headed the rescue effort.