Ma said that bad weather hindered rescue missions as last weekend's typhoon sparked three days of torrential rain, which grounded helicopters.
Rescuers on Friday struggled to rescue thousands of people trapped in mountain villages.
Liu Chao-shiuan, the prime minister, said flood-related losses were estimated to be around $3.4bn although he did not specify the type.
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.
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.
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.
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.