The warning followed Afghan reports Pakistani aircraft carried out bombing raids in Afghanistan's eastern Khost and Kunar provinces late on Friday, killing civilians.
Pakistan has so far refused to comment on the reports, instead accusing the Taliban of doing nothing to stop attacks against Pakistan by militants in Afghanistan.
"Terrorists are using Afghan soil with impunity to carry out activities inside Pakistan," said a foreign ministry statement that was unusually strong in its language.
Pakistan was often accused of harbouring Afghanistan's Taliban fighters before they swept to power last August when the western allies ended the 20-year war.
Since their takeover, Islamabad has led the way in pressing the world to engage with the religiously driven Afghan government.
It is not clear, however, whether Pakistan's new Prime Minister Shehbaz Sharif will be as supportive of the Taliban as his predecessor Imran Khan, the cricket star turned conservative Islamist leader who was ousted last weekend in a politically tumultuous no-confidence vote.
On Saturday the Taliban foreign ministry called in Pakistan's ambassador to complain about civilians killed, it said, in Friday's bombing raids.
Taliban spokesman Zabihullah Mujahid warned Pakistan "not to test the patience of Afghans on such issues and not repeat the same mistake again otherwise it will have bad consequences".
Afghanistan's largest news channel, TOLO News, showed images of children's bodies it said were killed in the airstrike.
The same channel showed protests by hundreds of residents of eastern Khost province condemning Pakistan and shouting anti-Pakistan slogans.
Pakistan has not confirmed any attack on Afghanistan and Sunday's statement slams the Taliban rulers for doing too little to stop Pakistani Taliban militants using its territory to attack Pakistan.
"In the last few days, incidents along Pak - Afghan Border have significantly increased, wherein, Pakistani security forces are being targeted from across the border," said the Pakistani statement.
Last week, seven Pakistani military personnel were killed in an ambush near the border later claimed by the Pakistani Taliban, known as the Tehreek-e-Taliban Pakistan, or TTP.
Militant attacks in Pakistan have been accelerating since the Taliban took power in Afghanistan.
The attacks have been claimed either by the TTP or by an Islamic State group affiliate, also headquartered in Afghanistan, but against whom the Taliban have been fighting.
By late March this year, Pakistan had endured 52 attacks by militants, compared to 35 in the same period last year, according to Amir Rana, executive director of the Pakistan Institute of Peace Studies, an independent think tank that monitors militant activity in Pakistan.
The attacks have also become deadlier. So far this year in Pakistan, 155 people have been killed in such incidents, compared to 68 last year.
The border between the two countries, known as the Durrand Line, runs the length of the 2670 kilometre dividing line.
The Durrand line runs through the region's ethnic Pashtun population, often dividing tribes and families between the two countries.
Established by the British in the 19th century, successive Afghan rulers have refused to recognise it as the official border, laying claim instead to Pakistani territory known as Khyber Pukhtunkhwa Province where ethnic Pashtuns dominate.
Since taking power, Afghanistan's Taliban have clashed on several occasions with Pakistan over a border fence Islamabad is building.
