While Pakistan's government overwhelmed by the scale of the disaster has struggled to reach aid to millions of people, Islamist charities with much smaller resources have moved in swiftly to fill the vacuum.
It would not be the first time the government has announced restrictions against charities tied to militant groups. Critics say any banned organisations often re-emerge under new names, with authorities uninterested in stopping their operations.
"The banned organisations are not allowed to visit flood-hit areas," Interior Minister Rehman Malik told Reuters. "We will arrest members of banned organisations collecting funds and will try them under the Anti-Terrorism Act."
Pakistani President Asif Ali Zardari and a senior U.S. senator warned on Thursday that militants were trying to promote their cause during the floods, similar to what happened after an earthquake in Pakistan Kashmir in 2005.
More than 4 million Pakistanis have been made homeless by nearly three weeks of floods, making the critical task of securing greater amounts of aid more urgent.
Eight million people are in urgent need of humanitarian assistance.
The floods have marooned villages, destroyed power stations and destroyed roads and bridges -- lifelines for villagers -- just as the government had made some progress in stabilising the country through offensives against Taliban insurgents.
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