Adjourning the hearing till Tuesday, the court also ordered Musharraf's medical reports to be submitted before it, Dawn online reported.
The government announced its decision to formally prosecute Musharraf
The three-member bench, led by Justice Faisal Arab, resumed the hearing of the high treason trial against Musharraf, who has been charged by the government with abrogating, subverting, suspending, holding in abeyance and attempting to conspire against the 1973 Constitution by declaring Emergency and detaining judges of the superior courts.
The court asked Musharraf's counsel to submit the statement regarding his absence from the hearing.
Musharraf's lawyer Anwer Mansoor said he was not able to meet his client and had no information regarding his absence.
The lawyer said Musharraf's health condition was known to all and that he would not be able to attend the hearing.
Musharraf's counsel said Sunday his client was ill and will not appear before the court Monday.
The special court warned Jan 1 it could issue a warrant for the arrest of the former military ruler if he again failed to appear before it Jan 2, after Musharraf did not turn up for hearing the second time in 10 days.
But Musharraf was moved to a hospital on his way to court Jan 2 as he suffered a "heart problem".
The government announced its decision to formally prosecute the former army chief for high treason Nov 17.
Earlier Monday, the Islamabad High Court rejected a petition seeking to restrain Musharraf from travelling abroad for medical treatment.
Musharraf seized power in 1999 in a bloodless coup and was president from 2001 to 2008, when he stepped down and went in self-exile to live in London. He returned to Islamabad in March 2013 to contest in parliamentary elections.
However, a court disqualified him from standing in the May 2013 general elections, which his bete noire, Prime Minister Nawaz Sharif - the man he had deposed - won.
Musharraf has been granted bail in four major cases, including that of former prime minister Benazir Bhutto's assassination.