New attempts are under way to negotiate the remaining militants' surrender but one Afghan commander said they were seeking to attach unacceptable conditions.
A local Afghan spokesman told the BBC that 50 militants had moved out in groups of two or three on donkeys, crossing high mountain passes.
It is unclear how many of the militants - followers of terror suspect Osama Bin Laden - are left in Tora Bora following concerted efforts to hunt them down.
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Defence Secretary Donald Rumsfeld said on Saturday that the allied forces had advanced about two kilometres (1.25 miles) during the past eight hours and 50 al-Qaeda fighters had surrendered.
The International Red Cross is concerned at the treatment of the captives and is seeking access to them.
Reports speak of mounting casualties among al-Qaeda's foreign militants, with one Afghan field commander telling Reuters he had seen 20 dead Chechens alone.
An Afghan spokesman quoted by the French news agency AFP said the bodies of 33 militants had been found since Friday.
According to US military commander General Franks, speaking from Florida, there are between 300 and 1,000 while Afghan fighters at the scene said they were facing between 500 and 600 al-Qaeda members.
One local tribal leader, named only as Ali, said he believed that Bin Laden himself was among them, holed up in a cave with up to 200 followers.
General Franks has conceded it is possible that Bin Laden might have already fled Tora Bora and escaped into Pakistan.
In other developments:
Fierce fighting
Our correspondent saw new bombing strikes by US aircraft on Saturday.
According to an Afghan spokesman, a "special push" was made overnight but one unconfirmed report said ground fighting had died off on Saturday to allow more time for negotiations.
The Pakistan-based Afghan Islamic Press said that five Afghan fighters were accidentally killed in a US air strike late on Friday.
Another Afghan source quoted by Associated Press said al-Qaeda was split internally, with Chechens among them wanting to keep fighting.
Fighting on the ground has been furious, with a 12-strong team of US special forces troops operating alongside their Afghan allies.
In one incident on Friday, two US troops were reportedly injured as they attacked a machine-gun nest although General Franks was unable to confirm the Afghan report.
US diplomacy
The Pakistan-based Afghan Islamic Press Agency has reported that Bin Laden left Tora Bora 10 days before the bombardment began.
US officials say the ferocity of the al-Qaeda resistance and reported sightings of Bin Laden indicated his presence, but Mr Rumsfeld has conceded they could not be certain he was still in Afghanistan.
"I have seen reports that people believe are from reasonably reliable sources that in one case suggest he's still in Afghanistan, in another case suggest he's out of Afghanistan," Mr Rumsfeld said.
The US defence secretary has arrived in Azerbaijan for talks on a tour which will also take him to Armenia and Georgia.
All three states have offered Washington the use of their airspace by military aircraft, and the US is promising economic aid in return.
He is going to Uzbekistan, which borders Afghanistan, on Sunday.