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 apex court 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 apex court bench headed by Justice Jawwad Khwaja, which is hearing the petitions against Musharraf, expressed its displeasure at the interim government's reply.
Khwaja observed that the court had been seeking an answer from the government for the past eight days and now the administration has said that it can do nothing.
Khwaja further remarked that in the future, the interim government might even say that it cannot file an FIR against Musharraf.
The bench put off the case till tomorrow, when the judges will hear arguments by Musharraf's lawyers.
In Pakistan only the state can initiate charges of treason, which can carry the death penalty. Meanwhile, Musharraf's lawyers were not allowed to meethim today at his residence, which has been declared a sub-jail, despite an order issued by the Supreme Court.
Prison officials posted at Musharraf's five-acre farmhouse at Chak Shahzad on the outskirts of Islamabad said the lawyers could meet their client only if they got a "no-objection certificate" from the Punjab government.
Musharraf was arrested last week after the Islamabad High Court revoked his bail in a case related to the detention of over 60 judges during the 2007 emergency.
He is currently being held at his farmhouse.
The former dictator returned to Pakistan last month after nearly four years of self-exile, promising to "save" the country from economic ruin and militancy.
However, he was barred from running in the May 11 general election, which will mark the first democratic transition of power in Pakistan's history.
Musharraf faces several serious criminal cases.
Lawyers have petitioned the Supreme Court to put him on trial for treason for imposing emergency and he faces charges related to the 2007 assassination of former premier Benazir Bhutto and over the death of Baloch leader Akbar Bugti in a 2006 military operation.
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