Musharraf floated the proposal during a meeting in New York with US Secretary of State Condoleezza Rice on Monday, which also touched on the issue of Iran and Pakistan's ongoing dialogue with rival India.
"The president offered to Dr Rice that Pakistan is prepared to make a fence along certain areas which are more amenable to incursions," Pakistani Foreign Minister Khurshid Kasuri said after the meeting.
Kasuri said the proposal was aimed at muting accusations that Pakistan has been sluggish in cracking down on fighters linked to Afghan's former Taliban regime.
The Taliban was ousted by US-led forces in late 2001, and the fighters have used bases on the Pakistan side of the border to launch a campaign of violence across Afghanistan in the run up to parliamentary polls on 18 September.
"We don't want anybody, ever, to say Pakistan is not doing enough," said Kasuri, adding that Pakistan would be prepared to erect the fence along the entire length of the border.
"Pakistan is prepared to make a fence along certain areas which are more amenable to
Pakistani Foreign Minister
"But what the president offered today was that, as a starter, we could have it in certain areas," Kasuri said.
"Pakistan can do nothing more than that to show how serious it is as far as preventing incursions."
Asked to describe Rice's reaction to the plan, Kasuri would only say: "She heard it out".
As for Afghanistan, the minister said his government had yet to hear a response from Kabul.
Last week, Pakistan said it was sending 9500 extra troops to the border ahead of the Afghan elections.
Some 5000 soldiers were to be deployed in the lawless tribal areas of North West Frontier Province and 4500 to Pakistan's
southwestern border in Baluchistan province.
Musharraf, a key US ally in the "war on terror", also told Rice of his concern over any US moves that could destabilise another Pakistani neighbour, Iran.
Washington is currently seeking to have Iran referred to the UN Security Council for possible sanctions over its suspected nuclear weapons programme.
"As a neighbour (and) a friend of Iran, we would want a peaceful resolution of this issue," Kasuri said.
"Already we've suffered a lot because of destabilisation in Afghanistan and we do not want another part of our border
destabilised," he said. "That is our primary concern."