Three people were killed in a protest on Tuesday
The call follows the deaths of several people in demonstrations which have turned violent.
The spiritual leader of the Taleban in Afghanistan, Mullah Mohammad Omar, has called for Muslims around the world to back them in their fight against the United States.
Pakistan's President, General Pervez Musharraf, said extremist action would not be tolerated. However, he added that law and order was not under threat.
A BBC correspondent in Islamabad says the government is signalling a new determination to clamp down on the protests.
However observers believe most of the pro-Taleban demonstrators are Pakistani religious hardliners, rather than Afghans.
Islamabad says it is overburdened with the 2.5m Afghans and had been deporting them before the attacks on the United States last month.
Call to Muslims
In his first statement since the strikes began on Afghanistan, Mullah Omar called on Muslims throughout the world to back the Taleban.
In a pre-recorded statement played to the BBC by Taleban officials, Mullah Omar said Muslims should not obey the United States, which had labelled them terrorists.
Their representative in Islamabad, Abdul Salam Zaeef, said the American planes warned the United States to halt the attacks.
"As long as America is shedding the blood of the Afghans, it will not be beneficial to America and we will see what come in the future, and of course, we also say if America is continuing attacks on Afghanistan, it will also will not be safe."
Violent protests
Three people were killed on Tuesday in protests in Pakistan against the US-led air strikes on Afghanistan.
The deaths occurred when police opened fire on a crowd of several hundred people who had stormed a police station in the town of Kuchlak, near Quetta.
The deaths in Quetta came as Pakistan arrested three prominent Islamic leaders allied to Afghanistan's Taleban movement.
There have been protests in many areas of Pakistan, including Lahore, Orangi Town and the city of Rawalpindi, near to the capital Islamabad.
There was also a large demonstration in the southern city of Karachi where about 5,000 demonstrators took to the street.
They chanted anti-US slogans, but there was no violence.
Reports say about 1,500 students marched in Islamabad, and several hundred turned out in Peshawar near the border with Afghanistan.
The BBC's Daniel Lak says mainstream Pakistani opinion does not support the anti-US rioters, or the Taleban.
But he says news of civilian casualties trickling out of Kabul will cause more widespread anger against the American and British raids.