MANILA, 9 January 2009 (IRIN) - Flooding in some parts of Mindanao has exacerbated the humanitarian situation on the island after nearly five months of deadly fighting between government troops and the separatist Moro Islamic Liberation Front (MILF).

Heavy rains have caused rivers in the Cagayan de Oro and Lanao del Sur provinces to overflow their banks, while flash floods were experienced in the cities of Gingoog and Iligan.

Almost 40,000 people have been affected in 30 villages, the National Disaster Coordinating Council (NDCC) reported on 8 January, with more than 900 homes damaged or destroyed.

Of the displaced, nearly 10,000 are in evacuation centres. Three children were reported dead or missing, it said.

Relief agencies under pressure

Even though the low-lying areas affected by flooding are not in conflict-affected areas, according to aid workers, the floods are compounding the ongoing humanitarian emergency. More than 300,000 people remain displaced in the conflict-affected areas, many of them living in shelters or with relatives outside government-designated evacuation sites.

Prevailing insecurity remains the critical factor in preventing the displaced from returning home.

"The heavy rains and flooding that began late last year have been an added problem," Glenn Maboloc, a spokesman for Oxfam, which is providing water and sanitation support in North Cotabato and Maguindanao provinces, told IRIN.

"There have been cases when our relief workers could not reach evacuation centres. It's been hard trying to reach those needing humanitarian assistance," he said.

Aid workers also expressed concern over whether emergency stockpiles were adequate to handle additional displacement should the flooding spread to conflict-affected areas.

President Gloria Arroyo, who visited the flooded areas this week, ordered local government relief agencies to step up relief operations on the southern island while the military pulled out some troops in conflict areas to help augment rescue efforts.

Upon returning to Manila, she ordered the release of additional funds to help rehabilitate the area, while designating Surigao Province in northwestern Mindanao a "state of calamity" after massive flood damage to the local farming sector.

Total damage to livestock and agriculture topped US$500,000 in two weeks alone, a government source told IRIN.

Funding crunch

Meanwhile, UN relief agencies and their partners on the ground continue to feel the strain of five months of fighting between the government and the MILF after a court blocked a proposed deal that would have given the MILF control over a large autonomous region.

Peace talks have been suspended, while bombs and grenade attacks over the Christmas and New Year holidays left more than 40 wounded, and this week MILF rebels razed over 30 homes in the town of Sultan Kudarat.

"The situation is becoming more and more dire. These UN agencies are also running low on funds and relief assistance. It has been five months and we don't see any immediate end to the fighting in the last year of President Arroyo," one defence official, who asked not to be named, told IRIN.

The MILF had said it did not expect to return to the negotiating table until Arroyo's term expires in 2010.

The military said it would continue its operations, aimed at crushing the 12,000-strong MILF so they could no longer carry out large-scale attacks.

In a year-end assessment report for internal security operations, General Alexander Yano, chief of staff of the armed services, said troops "have gained grounds against different security threats by derailing the capabilities" of the MILF and the smaller Abu Sayyaf, an Al-Qaeda-linked group blamed for the country's worst terrorist attacks and in some cases known to provide assistance to MILF fighters.

He also underscored the military's role in relief assistance, calling it a fresh policy shift that would continue this year.

"We must intensify our operations on the ground while facilitating cooperation with the communities involved," he said.

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