The caretaker administration, formed last month to conduct the May 11 general election, conveyed its position in a reply submitted to the Supreme Court.
Several lawyers have filed petitions seeking Musharraf's trial for treason and the SC had asked the government to state its position on the issue. In its reply, the caretaker government refused to put Musharraf, 69, on trial for treason under Article 6 of the Constitution.
The government said considering, deliberating or commencing any legal proceedings under Article 6 will be a move that is not part of its mandate.
The reply further said the government was busy providing security to candidates contesting the upcoming polls to the national and provincial assemblies.
An SC bench headed by Justice Jawwad Khwaja, expressed its displeasure at the interim government's reply.
The bench put off the case till Tuesday, when judges will hear arguments by his lawyers.
Meanwhile, Musharraf's lawyers were not allowed to meet him Monday at his residence, despite an SC order.