About six religious leaders filed a complaint with the Islamabad police, demanding that charges of unlawful interference in Pakistani religious schools be brought against the foreigners, who they said were FBI agents.
"We want these people charged. They illegally entered our madrasas and are interfering in the affairs of our religious institutions," said Abdul Rashid Qasi, the deputy head of a school that was not raided.
Police refused to say whether charges would be filed.
The government released a statement denying that the raids occurred but said the allegation would be investigated.
Khaista Gul, a 37-year-old cook at one of the schools reportedly raided, Madrasa Darul Uloom Subhania, said he was blindfolded and taken for a 10-minute drive. Questions about the Taliban and Al Qaeda were posed in English by the foreign men and translated, he said.
None of the students or teachers were detained, said Maulana Fida Mohammed, administrator of the school where Gul works.