Mamoor Khan, a police inspector, said the men had been collecting donations in the southern city of Karachi in the name of a charity, Al-Rahmat Trust, recently set up by the group Jaish-e-Mohammed.
"We arrested them because they are from Jaish-e-Mohammed, which is not allowed to carry out any activity," he said on Saturday.
President General Pervez Musharraf banned Jaish-e-Mohammed in January 2002 in an effort to crack down on certain groups the government considers extremist.
Also on Saturday, India and Pakistan started talks on an unprecedented opening of their disputed Kashmir border to help earthquake victims.
Foreign Ministry officials were meeting in Islamabad to discuss whether to allow Kashmiris to cross the heavily militarised Line of Control, the ceasefire line that divides the Himalayan region that the South Asian rivals have fought two wars over.
A joint statement was expected later on Saturday after the talks.
Jan Vandemoortele, the UN's humanitarian coordinator in Pakistan, said on Friday that opening the Kashmir border could help the relief effort - if not solve the logistical challenges posed by the formidable terrain.
Meanhwhile Queen Rania of Jordan, an envoy for Unicef, said the world community had a "moral obligation to do more to help victims of the quake, including thousands of orphaned children".
"If we do not act now thousands more innocent lives are going to die," she said during a visit on Saturday to Muzaffarabad in Pakistan-administered Kashmir.