"The participants reiterated support for the pivotal role of the president and COAS [Chief of Army Staff] in the ongoing reform process," read the statement, issued after Musharraf chaired a meeting of corps commanders in Rawalpindi.
The statement also referred to the mounting opposition, describing it as a "malicious campaign against institutions of the state, launched by vested interests and opportunists".
"Any attempt by a small minority to obstruct the aspirations of [the] vast majority would only derail the nation from its path of progress and prosperity," the military said in a statement.
Musharraf, who seized power in a bloodless military coup in 1999, will seek a second five-year term as president later this year.
Musharraf aims to be re-elected by the current assemblies before they are dissolved in November ahead of general elections. Political analysts suspect he also wants to remain army chief, although he is due to leave that role by the end of this year.
The two-month ban on rallies in Islamabad came amid signs that the government is growing increasingly intolerant of protests against the Musharraf's dismissal of Chaudhry.
"We have imposed a ban on rallies in Islamabad. A notification about it has been issued, and this step has been taken to ensure peace and avoid any inconvenience to the general public," Mohammed Ali, Islamabad's deputy chief of administration, said.
"It would be in the best interests of Pakistan for Musharraf to step down"
Jim ibarra, Cyberjaya, Malaysia
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Ali said there were no immediate plans to keep Chaudhry's supporters from joining him in a 50km procession from Islamabad to the city of Abbotabad on Saturday where the judge wants to address a gathering of lawyers.
However, television stations said they have been barred from covering the protest live.
Chaudhry has addressed similar gatherings since his suspension, but authorities stopped him from leading a rally in Karachi, triggering clashes which left 41 people dead May 12.
Under the ban, anyone wanting to organise a gathering of more than five people must get permission from the government.
Ali said no request had come from Chaudhry's supporters for the procession.
Aitzaz Ahsan, a lawyer for Chaudhry, said that no permission was needed. He said: "God willing, we will go to Abbotabad with the chief justice on Saturday, and we have no plan to apply for any permission."
Lawyers and supporters from Pakistan's opposition parties have held a series of rallies since Chaudhry's dismissal on March 9.