Pakistan has ordered all unauthorised Afghan asylum seekers - an estimated 1.7 million people - to leave the country by November.
A spike in attacks along the two countries' border, which Islamabad blames on Afghanistan-based operatives, has escalated tensions this year.
It has also fuelled resentment in Islamabad, which on Tuesday announced a crackdown on "illegal" migrants.
The Taliban government urged Pakistan to rethink its "unacceptable" move.
Afghanistan's rulers have repeatedly denied providing refuge for militants who target Pakistan.
Last week, a blast at a mosque in Mastung city, near the border with Afghanistan, killed at least 50 people during a religious celebration.
Pakistan's Interior Minister Sarfraz Bugti did not appear to directly reference that and another attack in Balochistan province when he announced the crackdown order on "illegal" Afghans on Tuesday.
The right to seek refuge in a foreign country is enshrined in international law. Pakistan has taken in hundreds of thousands of Afghan refugees during decades of war - particularly since the Taliban returned to power in Afghanistan in 2021.
About 1.3 million Afghans are registered as refugees while another 880,000 have received the legal status to remain, according to the UN.
But another 1.7 million people are in the country "illegally", claimed Mr Bugti on Tuesday - an apparent reference to those who have not yet gained refugee status.
He said those people would have to leave the country by the end of the month - whether voluntarily or through a forced deportation.
"If they do not go... then all the law enforcement agencies in the provinces or federal government will be utilised to deport them," he said according to state media reports. He did not provide further details on how such an operation would take place.
He also announced a taskforce aimed at identifying and confiscating private businesses and assets of "illegal" Afghans in the country.
But Afghan refugees are "not involved in Pakistan's security problems", said Zabihullah Mujahid, the spokesman for the Taliban administration in Kabul.
"As long as they leave Pakistan voluntarily, that country should tolerate them," Mujahid said on X, formerly Twitter.
Afghan officials in Pakistan said local authorities had already begun rounding up Afghans - both those with and without legal status to remain.
In a statement on X, formerly known as Twitter, its embassy said more than 1,000 Afghans had been detained in the past two weeks.
Balochistan province near Pakistan's border is an area which has frequently been hit by armed fighters including the Tehrik-e Taliban Pakistan (TTP) or the Pakistani Taliban, and the Islamic State militant group.
Earlier this month, at least 11 people - including a prominent Muslim leader - were injured in an explosion in the same district.
Local state outlet APP reported that Islamabad eventually wanted all Afghans in the country to leave - even those with legal status and Pakistan residence cards. It cited government sources for its report.
Mr Bugti said there had been 24 suicide bombings along Pakistan's border since January - more than half of which he blamed on militants operating from Afghanistan.
He announced tighter restrictions on Afghans entering Pakistan from 1 November - saying only visitors with visas and passports would be allowed in.
It has been custom for Afghans crossing into Pakistan at land borders to use their national identity cards as a travel document. There is a significant backlog of Afghans seeking documents to enter Pakistan - and obtaining visas and passports has turned into a months-long process.