The court, trying 70-year-old Musharraf on charges of high treason for imposing emergency in 2007, said the criminal procedure code was applicable in the matter.
On Wednesday, the court had reserved its verdict on the applicability of criminal laws.
Though Musharraf's legal team filed an application seeking a stay on the court's order summoning him to appear in person on January 16, the judges ruled that they could not change their decision.
It said Musharraf had been exempted from appearance thrice and that the former President's counsel had not submitted an application for his absence today.
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Prosecutor Akram Sheikh had on Wednesday said the Supreme Court had issued a ruling whereby all crimes under the Army Act fell within the domain of Pakistan's penal code. He argued the special court enjoyed all the powers of a High Court.
While presenting his arguments, Musharraf's lawyer Anwar Mansoor said the criminal code could not be applied to the treason trial.
The court observed the report did not mention that Musharraf had had a heart attack and that he was not in a position to appear before it.
Musharraf was taken to a military hospital in Rawalpindi on January 2 after he suffered a "heart complication" while being taken to the special court. He had skipped two earlier hearings after explosives were found near his home.
The former military strongman is currently barred from travelling abroad but there has been rampant speculation that he would be allowed to leave Pakistan for medical treatment.