ISLAMABAD — Raging floodwaters have inundated almost one-fourth of Pakistan, forcing the country’s military to switch its focus from fighting the Taliban in the country’s restive northern tribal belt to a massive rescue and relief effort.

Meanwhile, as Pakistan’s civilian government struggles to manage the disaster, the country’s Islamic charities, some of which the United States lists as terrorist organizations, have been filling the void, further complicating an already fragile security atmosphere.

At a news conference Thursday, Pakistan President Asif Zardari admitted the disaster would have an impact on the country’s security.

“There’s a possibility that negative forces could exploit the situation,” he said.

Some 60,000 Pakistani troops, backed by the air force and navy, are now engaged in rescue and relief operations in flood-stricken areas, especially in the Khyber Pakhtunkhuwa, which borders Afghanistan and is the epicenter of military operations by Pakistani and NATO forces fighting militants here.

In Swat, where the Pakistan Army launched a major offensive against the Taliban in May, guns have largely fallen silent as security forces focus on rescuing thousands of people trapped in different parts of the scenic valley. All major roads and bridges there have been washed away.

“This is true that the army is bearing the double brunt,” Maj. Gen. Athar Abbas, a spokesman for the Pakistan Army told GlobalPost. Abbas said the scenic Swat valley and adjoining districts of troubled South Waziristan had all been badly affected by torrential rains and flash floods.

Analysts worry that the Taliban, driven out of the Swat region by persistent shelling from the Pakistan Army over the spring and summer, might use the opportunity to resettle there.

The swollen rivers have also cut off NATO supply lines, hindering the international security force’s ability to reach war-wracked Afghanistan.

The persistent rains and floods, which began July 22 in Baluchistan Province and which have continued unabated, have so far affected more than 20 million Pakistanis, from the snow-capped mountains in the north to the warm waters of the south. About 1,600 Pakistanis have been killed in the disaster, one of the region’s worst in recent memory. International aid officials put the estimated cost of the damage at between $10 billion and $15 billion.

Military operations in South Waziristan, a stronghold for the Pakistani Taliban and various other Al Qaeda-linked groups, have also reached a near standstill as floods cut off the districts of Dera Ismail Khan and Tank, which both serve as important supply routes for security forces in the troubled region.

“First thing first. We cannot see our countrymen in misery. The army chief has issued very clear orders that immediate rescue and relief operations are the army’s first priority,” Abbas said.

Abbas said it was too early to tell, but that so far there had been no major setbacks in the army’s operations against the Taliban in the two regions.

“We are fully taking care of security issues as well. We are making sure that these elements [the Taliban] do not take advantage of this situation,” he said.

Hamid Mir, an Islamabad-based security analyst, however, said there was little doubt that the Taliban and other Al Qaeda-linked militants were benefiting from the army’s shift in focus.

“There are reports that various army checkpoints have been washed away in adjoining districts of South Waziristan and Swat,” he said in an interview. “It’s a great challenge the army is facing. It has to fight militants and floods simultaneously. And this is not at all a walk in the park.”

Both of NATO’s primary supply routes, which lead from the southern port city of Karachi to the Afghanistan border, have also been totally submerged, analysts in the area said.

“NATO supplies have been totally suspended because of massive flooding at various spots. I have personally seen these highways inundated in waist-deep water,” Mir said.

Pakistani and NATO security officials denied the floods had caused supply problems.

As the Pakistan Army and the civilian government scramble to respond to the disaster on a national scale, the country’s numerous Islamic charities, many of which are linked to militant organizations, have been quick to respond on a local level.

Pakistan’s media has continuously highlighted the large relief effort undertaken by the Al-Khidmat Foundation, an aid group controlled by one of the country’s largest Islamic political parties, Jammat-e-Islami, Jammat-ul-Dawa’h. Investigators blamed the party for the deadly 2008 attacks in Mumbai, India, that killed more than 170 people.

Maymar Trust, which the United Nations and the Pakistan government have tried to outlaw because of its links to the Taliban, has also received positive press reports for its relief activities in local communities.

Over 20,000 volunteers from these organizations are now rescuing stranded people in flood-hit areas. The groups have also set up refugee camps, arranging food and shelter.

“I don’t care whether they are hardliners or liberals. What I know is that they were the first who reached us,” said Ameer Khan, a farmer.

Sitting in a makeshift hut at a relief camp run by Jammat-ul-Dawa’h in Mardan, about 25 miles west of Peshawar, Ameer gets two meals a day - one early morning and another at sunset - along with 400 other refugees, all of whom are now observing Ramadan, the Islamic holy month where observers fast during daylight hours.

Militant-linked charities like these have set up hundreds of relief camps in all four provinces of Pakistan, analysts said.

“A total failure of secular parties, especially those in the government, has created a political vacuum,” Mir said. "Someone has to fill this vacuum and if the religious parties continue to carry out their relief activities like this, they may fill that vacuum."