At least 35 people died, and farms and infrastructure suffered severe damage, officials said.
Of the island’s 20 provinces, the worst affected were in the north, including Misamis Oriental, Lanao del Norte, Agusan del Sur, Agusan del Norte, and Davao del Norte.
According to the National Disaster Coordinating Council (NDCC), more than 750,000 people had been affected by flash floods, landslides, storm surges and accidents at sea due to heavy rains that battered the area from 2 to 17 January.
Over 200,000 people remain in evacuation centres, while many areas have yet to be reached by aid agencies.
Many of the fatalities were in towns in the north-eastern section of mineral-rich island, which bore the brunt of the flooding and where forest cover has diminished over the past decade due to excessive logging and mining.
Eleven towns in the area remain under a "state of calamity", including Surigao City, Cagayan de Oro, and Gingoog City where flood-waters in some parts reached 1.5m, officials said.
"The trees supposedly meant to hold rainwater including loose boulders or rocks and soil from mountainsides are no longer there, so who's going to hold them?" asked regional disaster response chief Blanche Gobenciong.
"That is why areas that were low-lying were the ones greatly affected by flooding and landslides.”
The region's more than 500,000ha of forests were fast being lost to illegal logging concessions and mining operations, and there was now widespread clamour to replace local environment officials, she said.
Victoria Plaza, a former log trader, said police officers were routinely bribed to allow so-called "hot logs" or timber to pass through security checkpoints, turning a blind eye to logging activities that were not sustainable.
"Protection money comes from big timber processing plants. Controls are weak, and now we are paying for it," Plaza said.
In the northern province of Misamis Oriental alone, at least 27 elementary schools and nine daycare centres have been destroyed by flood-waters.
Provincial governor Oscar Moreno recommended the strengthening of infrastructure such as national highways and bridges which initially appeared undamaged but on closer inspection had suffered scouring.
A portion of a highway going into Gingoog City "was ripped" and taken by raging floodwaters, he said.
"There was already a scouring underneath which we failed to check earlier," he said. "Let's not wait for these infrastructures, like for example the bridge in Lugait, to collapse before we do something," Moreno added.
|Mindanao is the second-largest island in the Philippines, an archipelago of more than 7,000 islands
Meanwhile, Environment Secretary Lito Atienza told IRIN he had directed the suspension of new environmental clearance certificates to small- and medium-scale mining and logging concessions on Mindanao.
"While climate change is a reality, we also have to look at the possibility that illegal activities such as illegal logging and illegal mining may be the main factors for the disaster," Atienza said, adding that he had ordered a comprehensive study of the flooding that swamped the area.
"Until the study is completed, there will be no additions of certificates in the region," he said.
He said he has also begun an investigation into alleged corruption relating to timber and mining licences, and vowed to prosecute those found guilty.
"If these unfortunate happenings were brought about by abuse of our natural resources and environment, we should be held responsible," he said. "We have to ascertain and make sure, that is why we are carrying out this investigation."
World Food Programme (WFP) country director Stephen Anderson said his agency had agreed to provide up to 630MT of rice to assist about 25,000 families affected by the disaster.
The decision was made after a WFP team found that people in evacuation centres were "highly vulnerable due to growing food insecurity".
"WFP fully understands that the situation remains fluid, and we will continue to work closely with government and the NGOs on the ground to further assess and adjust our response accordingly," Anderson said in a statement.
"The restoration of livelihoods of the affected people could take time; hence, WFP announces this response in hopes that the food support could provide immediate relief to the situation," the agency official said.
This article was produced by IRIN News while it was part of the United Nations Office for the Coordination of Humanitarian Affairs. Please send queries on copyright or liability to the UN. For more information: https://shop.un.org/rights-permissions