The case, brought up in petitions challenging Musharraf's imposition of emergency rule and firing of the judges that year, could lay the groundwork for future action - even a trial - against the one-time military ruler.
It could also rattle Pakistan's political scene at a time when the U.S. wants the nuclear-armed nation to focus on fighting al Qaeda and the Taliban along the Afghan border.
Pakistani Attorney General Sardar Latif Khosa confirmed the court order.
He said the federal government would not defend the actions taken by Musharraf on Nov. 3, 2007, when faced with growing challenges to his rule, he declared a state of emergency, suspended the constitution and dismissed the judges.
Musharraf is currently staying in London with his family. He could not immediately be reached for comment. The next hearing in the case is on July 29.
Wasi Zafar, a law minister during Musharraf's rule, said the retired general could appear before the Supreme Court either through his lawyer or in person.
"If he does not do it, the court can initiate proceedings against him in his absence," he said.
The former army chief seized power in a 1999 military coup and became a critical, and criticized, U.S. ally following the Sept. 11, 2001 attacks that sparked the American-led invasion of neighboring Afghanistan.
In early 2007, Musharraf dismissed the Supreme Court's chief justice, Iftikhar Mohammed Chaudhry. That triggered mass protests led by lawyers that damaged Musharraf's popularity.
The court managed to bring Chaudhry back, but - faced with growing rancor - Musharraf declared the emergency, tossing out Chaudhry and around 60 other judges. That only deepened popular anger against the military ruler.
Under domestic pressure, and prodding from the U.S., Musharraf lifted the emergency rule after about six weeks, stepped down as army chief and allowed parliamentary elections to take place the following February.
The elections brought his political foes to power, and they ultimately pushed him to resign the presidency in August 2008.
But the fate of the judges, especially that of Chaudhry, has caused fissures among those who came to power.
A coalition government consisting of Asif Ali Zardari's Pakistan People's Party and Nawaz Sharif's Pakistan Muslim League-N fell apart over the slow pace of reinstating the ousted jurists.
Ultimately, facing escalating lawyer-led protests reminiscent of Musharraf's era, now-President Zardari agreed to reinstate Chaudhry - whom he'd viewed as too political a figure - in March.
Ever since, there have been rumblings in some corners about whether and when Musharraf would have to answer in court for his actions, and court petitions were filed over the issue.