Pakistani attitudes to the Taleban are hardening
General Musharraf made the comments during an address to ministers and heads of the armed forces.
BBC Islamabad correspondent Susannah Price says this sounds similar to the kind of post-Taleban administration being discussed by members of the US-led coalition against terrorism.
It comes as US Defence Secretary of State Donald Rumsfeld continues a tour of Arab countries to gather support for possible attacks on Afghanistan.
On Wednesday, he was in Saudi Arabia, and is continuing to Egypt on Thursday.
In other developments:
New Afghan alliance
Pakistan is the only country which still recognises the Taleban.
Western diplomats have been courting the former Afghan King, Zahir Shah, and the opposition Northern Alliance have indicated they would be ready to work with him.
The 86-year old former monarch, who was deposed in 1973, lives in exile in Rome.
The former king has welcomed General Musharraf's invitation to send a representative to Islamabad for talks.
In his address, General Musharraf stressed that a new government should be multi-ethnic, unlike the Taleban, who are dominated by Afghanistan's largest ethnic group, the Pashtuns.
Analysts say that the general's remarks may be a way of preparing Pakistanis for military action in Afghanistan.
If the American attacks cause civilian casualties, General Musharraf could face increased opposition at home for his backing of the United States.
Pakistan studies evidence
The general's remarks followed an announcement by the Pakistani Government that it was studying evidence from the United States linking Osama bin Laden to last month's attacks in America.
Bin Laden is thought to be hiding in Afghanistan.
But the Pakistani Foreign Ministry says it cannot yet say if the evidence proves Bin Laden's links to the 11 September attacks on New York and Washington.
Meanwhile, leaders of Pakistani religious parties are reported to have cancelled a trip to the Taleban headquarters in the Afghan city of Kandahar because they have given up hope of negotiating an end to the crisis.
A spokesman for Jamaat-e Islami told the Associated Press news agency that the leaders, all clerics, saw no chance of ending the deadlock over the Taleban's refusal to hand Bin Laden over to the United States.
Pakistan has offered substantial military co-operation to Washington in its war against global terrorism.
In return, the US has dropped sanctions against Pakistan.
But General Musharraf has also insisted that Pakistan should see proof of Bin Laden's guilt before any military action is taken in Afghanistan.