Ms Tong is now shuttling between MSF clinics in the small border town of Iskasheim and the provincial capital, Faizabad, to help refugees displaced by the war with the Taleban.
But she said the option of escape through neighbouring Tajikistan still remained open.
Eleven MSF medicos did take the chance to leave the country this week, leaving a skeleton staff of six, who are maintaining intermittent e-mail contact with the outside world via a satellite phone, use of which has been declared an offence punishable by hanging by the Taleban.
Sam Cunningham, a close friend, said Ms Tong has had plenty of experience in war zones including service in Sierra Leone and Kosovo.
She had thanked the Chesterton family, New Zealand aid workers who left Faizabad for Peshawar in Pakistan, for the gift of a large supply of vegemite.
Ms Tong's decision to stay comes as the Taleban acknowledged for the first time the turmoil created within Afghanistan by the threat of an American attack.
The movement's leader, Mullah Mohammed Omar, yesterday called on people not to leave the cities.
UN agencies say the disruption has added to an already critical situation in a nation crippled by three years of drought.
Before Afghanistan became the focus of world hostility for its sheltering of Osama bin Laden, America's prime suspect for the terrorist attacks a fortnight ago, 3.8 million Afghans were already dependent on food aid.
Another five million were malnourished, and more than a million displaced within the country. Now the UN expects one million new refugees to head for Pakistan and 400,000 for Iran, which has also closed its border.
In Geneva the United Nations High Commissioner for Refugees appealed yesterday for $US252 million ($626.5 million) to care for Afghan refugees, and the EU proposed almost doubling its aid to $US46 million, money Pakistan and Iran will need urgently if and when they allow the borders to open.
With the United Nations warning of a looming humanitarian catastrophe of "stunning proportions" in Afghanistan, Pakistan, with two million Afghan refugees already on its soil, yesterday conceded that it might open the border "if the situation becomes untenable, or if there is an attack", said the minister responsible for refugees, Abbas Sarfraz.
Aid officials said some 5000 refugees who had reached the no man's land between the two border posts at Chaman, near the Pakistani city of Quetta, had been pushed back into Afghanistan.
"This week, two women who had given birth in the open at Chaman were allowed into Pakistan for humanitarian reasons," said Yusuf Hassan, UNHCR regional spokesman. "But as soon as they were able to walk, they and their new-born babies were taken back to the border and pushed across."
Map: Opposing forces in the war against terror
Afghanistan facts and links
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