Ma said the whole nation would mobilise to help the victims, saying: "The government will overcome all obstacles to accomplish the mission."
For his part, Liu Chao-shiuan, the prime minister, said flood-related losses were estimated to be around $3.4bn although he did not specify the type.
More than 50,000 soldiers deployed to remote areas continue to battle raging rivers and fallen bridges to reach victims trapped in southern and central Taiwan.
Waiting for rescue
Local media is reporting that dozens of communities in southern Taiwan cut off by the storm are still waiting for rescue, nearly a week after the deluge.
Relief workers in the south of Taiwan have struggled to reach many areas, where roads have been cut by landslides and bridges washed away.
Authorities earlier said the official death toll from the storm had risen to 116. But government officials said the figure did not include an estimated 300 people believed to have been buried in a mudslide in Hsiao Lin, one of the worst-hit mountain villages.
"The county magistrate gave the premier a report that in his judgment about 300 were dead," the Reuters news agency reported, quoting the head of Taiwan's government information office.
"These are the conditions now. Specific numbers will depend on the army opening the road and sending people in," the official said, in reference to Hsiao Lin.
Stephen Chen, the secretary-general of the Taiwan Red Cross Society, said rescue teams are searching for survivors in Hsiao Lin.
But he told Al Jazeera that heavy rains were hampering search efforts, even though they have eased in some parts of the island.
"If the weather gets better, then we can have more rescue teams going to the village," he told Al Jazeera on Friday.
In addition, Chen said, rescue teams need better resources, including newer helicopters, to tackle the recovery operation.
"Some of our helicopters are too old for these rescue needs. This kind of helicopter is more than 30 years old, and is not good enough. So we would like to have better helicopters."
Meanwhile, pressure is mounting on the government to speed up rescue and recovery efforts.
Many survivors from the hardest hit areas have said more lives could have been saved if authorities had acted more quickly.
At one rescue centre tempers flared as relatives desperate for news of missing loved-ones fought with police and soldiers as they tried to storm their way on to helicopters heading to the disaster zone.
| Taiwan has issued an appeal for international help as it steps up rescue efforts [AFP]
Newspaper editorials in Taiwan have also criticised the official response to the disaster - saying Ma was too slow to send in troops to help.
But the government has said it is ready to put more money into the rescue efforts and already has plans for rebuilding communities devastated in the storm.
Al Jazeera's Steve Chao, reporting from Kaohsiung county - one the hardest-hit regions - said it is difficult to gauge how accurate the criticism has been.
"We saw a huge presence of rescue workers and aid organisations and we saw a lot of the military soldiers working very hard ..., so it is difficult to get a true picture of how well or how poorly co-ordinated the relief effort has been," he said.
"We are aware of at least two communities that were not so much ignored, but did not receive aid fast enough.
"Some of the survivors were forced to live on water that they could find for themselves before aid arrived.
"So there is criticism. How real or true this is is still difficult to say. We will get a clear picture of that in the coming days."
The government issued an appeal on Thursday for international help, including heavy-lift helicopters, as part of efforts to locate and rescue the thousands of people still missing or stranded across the island.