Catastrophic floods in Pakistan have killed more than 1,500 people, displaced at least 12 million, and left 20% of the country under water. Though the World Bank and the United Nations have pledged more than $1.4 billion in combined relief funds, the international community has generally been reluctant to get involved with the troubled Pakistani government. All too eager to aid flood victims, however, are Pakistani terrorist groups that use social services to expand their influence.

As the floods worsened this month, Islamabad’s recently formed National Disaster Management Agency proved weak and inexperienced, and President Asif Ali Zardari remained abroad and seemingly out of touch. Meanwhile, hard-line Islamic charities tied to terrorist groups sent thousands of volunteers to undertake relief efforts in the most affected, hard-to-reach areas.

Within days, groups including Falah-e-Insaniyat, the charitable arm of Lashkar-e-Taiba (LET)—which carried out the 2008 Mumbai terrorist attack—were serving meals to victims and providing them with clothing, medicine and even money. In another instance, the Haqqania Madrasa, a fundamentalist boarding school that proudly counts senior Taliban among its alumni, has converted itself into a shelter and is giving meals, electricity and medical treatment to at least 2,500 victims.

There is already evidence that such activities are earning these groups public support from Pakistanis all along the Indus River basin, which spans the entire country. “For us they’re angels,” one retired policeman told Reuters.

So history is repeating itself. The same thing happened in October 2005, after a massive earthquake struck Pakistan. With the Pakistani government’s initial response slow and disorganized, victims in remote areas relied on extremist groups for immediate rescue. Militant groups like Jamaat-ud-Dawa (the political arm of LET and a U.N.-listed terrorist organization) and the Al Rasheed Trust (an organization under U.N. sanction for its links to al Qaeda) were the first to reach isolated areas with water, food and medicine. These groups later set up tented villages and mobile hospitals, and helped care for orphans.

Even as some Pakistanis applauded American aid and personnel, entire villages benefited directly from the aid of as many as 17 extremist groups linked to terrorism or officially banned by the Pakistani government. Reports quickly circulated describing the many victims grateful for these groups’ widespread relief efforts, with Pakistan’s Interior minister even remarking that they were the “lifeline of [Pakistani] rescue and relief work.”

Though difficult to quantify, it’s hard to ignore the long-term impact of this phenomenon. While dispensing aid in 2005, extremist groups advertised for donations in mainstream Pakistani publications. They built orphanages and madrassas for victims, raising concerns among counterterrorism experts about recruitment and radicalization. Extremists gained trust among common Pakistanis and expanded their influence, gaining footholds in areas where they previously had only a limited presence.

The Pakistani people need help, even if it is coming from extremists. As such, it’s no surprise that U.S. officials have thus far not condemned these groups’ relief efforts. Washington has committed over $70 million in aid and is sending food, helicopters and a special “Disaster Assistance Team” to the region—all to address the humanitarian crisis and to improve Pakistani opinion of America. Still, militant extremists may well emerge from the floods as Pakistan’s saviors.

What happens—to the U.S. mission in Afghanistan, among other things—if even more Pakistanis sour on their government? How concerned should Americans be if the group that perpetrated the Mumbai attack uses relief work to expand its recruiting base in northwest Pakistan?

Such pressing questions make it all the more important that the international community approach this crisis generously and responsibly. Moving forward, it will be critical to demand transparency from groups that receive aid to distribute, and to insist that the Pakistani government crack down on the charitable activities of terrorist organizations. It will also be crucial to empower, through money and programming, local nonprofit groups that could become sources of alternative relief during the next crisis.

Of course, even the best reconstruction efforts may have little effect on how Pakistanis view their own government or the U.S. At this point, many have already pledged their support to another team.

Ms. Porges, a former fellow at the Council on Foreign Relations, has served as a policy adviser in the Defense and Treasury departments.