Media reports said the imam of Sultan Masjid, one of Karachi's biggest mosques, declared Rehman a 'kaafir' (infidel) and 'wajib-ul-qatl' (fit to be killed) while delivering a sermon after the Friday prayers.
The mosque has close ties to the Saudi Arabian government.
Islamic hardliners who organised a massive rally in Karachi today also issued a pamphlet that named Rehman as a person who "has invoked the religious honour of Pakistan's Muslims" for calling for changes in the blasphemy law.
The threats came days after a police guard gunned down Punjab Governor Salmaan Taseer for criticising the blasphemy law.
Civil society activists today filed a complaint against the imam of Sultan Masjid at the Darakhsan police station in Karachi.
The complaint was registered on behalf of Rehman, a senior leader of the Pakistan People's Party, Salmaan Taseer's son Shaan Taseer and journalist Ali Chishti.
In the complaint, the civil society activists alleged that the imam of Sultan Masjid had also lauded Mumtaz Qadri, the policeman who assassinated Salmaan Taseer.
The civil society activists said they were proud to be Muslims but rejected murdering people in the name of Islam.
Hardliners have been gunning for Rehman since she tabled a private bill in parliament to remove the mandatory death sentence for blasphemy.
Reports have said Rehman has been facing pressure from within the PPP to leave Pakistan for her own security.
Security has been enhanced at Rehman's residence in Karachi and she has told the media she will not leave Pakistan.
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