MQM leaders Mohammad Anwar, Muazzim Ali, Kashif, Syed Mohsin Ali and Khalid Shameem have also been nominated in the FIR.
According to the text of the FIR, the conspiracy for the murder of MQM leader Dr Imran Farooq was hatched in Pakistan.
The case filed by the counter-terrorism section of the investigation agency has been regisered under clause 7 of the anti-terrorism act (ATA).
Interior Minister Chaudhary Nisar Ali Khan had earlier said that the federal government has decided to lodge a case in Dr Imran Farooq murder case in Pakistan.
Dr Farooq, a senior leader of MQM, was murdered outside his residence in London in 2010.