The court order came two weeks after the apex court declared his move as 'unconstitutional'.
District and Sessions Judge Akmal Raza issued the order in Islamabad after lawyer Aslam Ghuman filed an application in his court asking for a case to be registered against Musharraf, who is currently in Europe.
This is the first time that a court has asked police to register a case against Musharraf.
Several persons, including relatives of people detained by intelligence agencies, have approached police for registering cases against Musharraf but officials have been reluctant to act.
In his application, Ghuman accused Musharraf of illegally detaining over 60 judges, including Supreme Court Chief Justice Iftikhar Chaudhry, after imposing emergency.
Ghuman also complained to the judge that police were reluctant to act on his request for an FIR to be registered against Musharraf.
Ghuman said he had filed a complaint with a local police officer some time ago but no action was taken. The judge ordered that the case should be registered
by the Secretariat police station in the heart of Islamabad.
Ghuman later visited the police station, where the station house officer accepted his application and recorded his statement. The SHO told reporters the FIR would be registered once the police station received the court's order.
Pakistan's Supreme Court ruled on July 31 that the emergency proclaimed by Musharraf was 'unconstitutional and illegal'. The verdict has raised the possibility of the former President being tried for treason.
However, only the government can initiate such a trial. The apex court had asked Musharraf to appear in person or through a lawyer to explain his position but the former military ruler ignored the notice issued to him.
Over 60 judges were sacked and placed under house arrest after they refused to take oath under the Provisional Constitutional Order through which Musharraf suspended the constitution and imposed emergency.
The deposed judges were restored to their positions after the opposition PML-N and the lawyers' movement organised nation-wide protests on the issue in March this year.
Musharraf resigned in August last year to avoid being impeached. He left Pakistan in April to deliver a series of lectures abroad. PML-N chief and former premier Nawaz Sharif has demanded that the government should put Musharraf on trial for suspending the constitution.