Judge Rana Nisar Ahmed of the Rawalpindi-based court summoned Federal Investigation Agency Director Wajid Zia to explain the non-compliance of the warrant issued for Musharraf during proceedings conducted at Adiala Jail yesterday.
Criticising the inordinate delay in serving the warrant, the judge asked Zia to appear before him with an explanation at the next hearing on Apr 9.
Zia is the chief of the joint investigation team probing Bhutto's assassination.
During the last few hearings of the case, the judge has repeatedly asked the FIA to serve the arrest warrant for 68-year-old Musharraf, who has been living in self-exile in Britain since 2009.
The Express 24/7 news channel reported that the British government had refused to extradite Musharraf to Pakistan, citing the absence of an extradition treaty between the two countries.
The FIA handed over to the anti-terrorism court a report received from the British Home Department, the channel reported.
The anti-terrorism court issued an arrest warrant for Musharraf in February after investigators declared him an "absconder" and told the judge that the former military ruler was not cooperating in the probe into the assassination.
Investigators have alleged that Musharraf''s regime had failed to provide adequate security to Bhutto after she returned to Pakistan from self-exile in 2007.
During yesterday's proceedings, which were held behind closed doors, FIA Deputy Director Khalid Rasool told the judge that authorities had sent a letter to the British High Commission asking it to send back Musharraf's arrest warrant.
"We have sent them a fresh letter requesting the British authorities to send back the arrest warrants, whether served or not," he was quoted as saying by The Express Tribune newspaper.
FIA prosecutor Chaudhry Azhar said it seemed that there "is a Musharraf sympathiser...in the Foreign Office who may be impeding" the serving of his arrest warrant, the report said.
The FIA has so far submitted three separate charge-sheets in the assassination case.