While the government, overwhelmed by the scale of the disaster, has struggled to reach aid to millions of people, banned outfits with much smaller resources have moved in swiftly to fill the vacuum.
"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."
President Asif Ali Zardari and a senior US senator warned on Thursday that militants were trying to promote their cause during the floods, similar to what happened after the earthquake of 2005 in Kashmir.
Eight million people are in urgent need of humanitarian assistance.
The United States led a stream of pledges of more funds for Pakistan during a special meeting of the UN General Assembly on Thursday. US Secretary of State Hillary Clinton promised a further $60 million, bringing to more than $150 million the contribution Washington would make towards emergency flood relief.
US Senator John Kerry, who visited flood-hit areas with President Zardari on Thursday , said action must be taken to prevent anyone from exploiting frustrations.
"We need to address that rapidly to avoid their (Pakistani's) impatience boiling over, and people exploiting that impatience and I think it's important for all of us to understand that challenge," Kerry said, in a clear reference to the Taliban. "We also share security concerns."
The United States needs a stable Pakistan, which it sees as the most important ally in the war against militancy, especially in neighbouring Afghanistan, where a Taliban insurgency is raging.
In a sign of growing concerns over the ramifications of the floods, Kerry said $200 million from the $7.5 billion US aid package for Pakistan over five years, which he co-authored, would be diverted to the relief effort.
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