72-year-old Musharraf last month flew to Dubai for purported treatment after the Supreme Court lifted bars on his foreign trips.
Musharraf's lawyer Akhtar Shah submitted the former army chief's April 6 medical report along with a request to grant his client temporary exemption from appearing in court in Rawalpindi but the judge rejected both and upheld his non-bailable arrest warrants issued earlier this month.
Anti-terrorism court (ATC) judge Sohail Ikram maintained that the former military ruler left the country in March but the report presented in the court is of April.
Islamabad police, in its report regarding Musharraf's non-bailable arrest warrants, stated that the warrants could not be executed as he is in Dubai since March.
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The Judge ordered Inspector General Islamabad to find his whereabouts and produce him in court on May 20 when the next hearing of the case will be held.
Police registered the judges detention case on August 11, 2009, against Musharraf, who is accused of detaining at least 60 judges of the superior courts in their residences for over five months after imposing emergency in 2007.
Musharraf ruled from 1999 to 2008 when he stepped down.
He lived abroad for most of the time until his return in 2013 to contest elections but was implicated in several high- profile cases and was not allowed to leave the country.
Musharraf had said before leaving that he was going abroad to seek medical treatment for a spinal cord ailment which has now developed several complications and will "come back in a few weeks or months".
The ex-army chief is facing a slew of court cases. Apart from the illegal detention of judges case, he is facing trial in high treason case for abrogating the constitution in 2007. Treason is punishable with death in Pakistan.