Kausar Abbas Zaidi, a judge in the country's anti-terrorism court, ordered Musharraf to appear in court May 4, Dawn News reported.
Local authorities said he would be held at his fortified villa outside Islamabad, which they declared a "sub-jail."
Musharraf is the first former army chief of army and the first head of state to be arrested in Pakistan.
He had jailed more than 60 judges, including the country's chief justice, for more than six months after proclaiming a state of emergency in the country Nov. 3, 2007, the BBC reported.
Separately, Musharraf is accused of conspiracy in the assassination of Benazir Bhutto in 2007 and the 2006 slaying of a Balochistan nationalist leader.
He returned to Pakistan last month after nearly four years of self-imposed exile in a reported bid to run for president. Election officials barred his candidacy.
Musharraf arrived at the court under heavy guard by police and paramilitary soldiers, and left the same way, The New York Times reported.
Taliban militants have threatened to kill him.
Musharraf is being tried in anti-terrorism court after the High Court ruled the charges against him amounted to terrorism.