On Wednesday, helicopters airlifted out some of the nearly 1,000 survivors who had made it to higher ground before walls of mud and rock covered their homes in at least three villages.
But continuing heavy rains made it slow-going and dangerous, with helicopters only able to make a few dozen trips to bring some of the survivors to safety in Cishan in Kaohsiung county, where a makeshift landing zone has been set up at a school.
Highlighting the continuing danger, the funerals were held on Thursday for three rescue workers killed earlier this week when their helicopter crashed into a mountain in heavy fog.
In Hsiao Lin, one of the worst hit mountain villages, hopes of finding survivors faded after rescue teams found nearly the entire village wiped out by a mudslide.
Al Jazeera's Steve Chao, reporting from Hsiao Lin, said the entire place had been enveloped by mud and only two out of about 200 homes remained standing, the rest either completely covered or washed away.
Only about 50 villagers managed to escape by climbing up to higher ground and more than 600 people were believed dead, witnesses said.
The mudslide occurred on Sunday morning when many people were still asleep and the village was more populated than usual because many children had returned to celebrate Father's Day in Taiwan on Saturday.
Rescuers arrived on Wednesday after battling through washed-out roads, unstable terrain and bad weather for days, but found little in the village left to rescue.
| Rescuers have been trying to get to villages on foot after roads were washed out [AFP]
Villagers in the south appeared to have been taken by surprise by Morakot's arrival as the typhoon had been forecast to head north, but instead turned south to unprepared areas, our correspondent said.
Morakot, which had earlier killed at least 21 people in the Philippines, triggered the worst flooding in Taiwan in 50 years over the weekend before moving on to China.
It later weakened to a tropical storm but still wreaked havoc on China's southeastern coast, triggering massive landslides and forcing the evacuation of about 1.5 million people from the provinces of Zhejiang and Fujian.
It also damaged or destroyed more than 10,000 homes and flooded over one million acres of cropland, China's civil affairs ministry said.