Afghanistan's warning came on Sunday after officials said more than 300 heavy artillery shells and rockets were fired from Pakistan into Afghanistan's eastern Kunar province over two days, killing at least four people.
Last month, a barrage of cross-border fire from Pakistan into Kunar forced thousands of villagers to flee their homes after Islamabad accused Kabul of protecting militants who infiltrated to kill 13 Pakistani soldiers.
Afghanistan and Pakistan typically blame each other for violence by Taliban Islamic militants plaguing both sides of their border, known as the Durand Line.
NATO's International Security Assistance Force "condemns the indirect fire attacks from across the Durand Line", ISAF said in a statement late Wednesday.
"We continue to work with the Afghan ministry of defence, and the Pakistan government to ensure an end of these attacks."
ISAF welcomed the announcement by the Afghan foreign ministry that talks on the issue would be held soon between officials from both sides in Afghanistan's eastern city of Jalalabad.
Pakistan on Sunday denied Afghanistan's charge of cross-border shelling, calling it "incorrect".
"Pakistani troops only respond to and engage militants from where they are attacked/fired upon," said a senior military official in Islamabad.
Over the last year he said at least 15 cross-border attacks were carried out by militants against Pakistani check points and the civilian populations in northwestern towns of Dir and Chitral.
NATO has some 130,000 US-led troops in Afghanistan helping the government of President Hamid Karzai fight Taliban Islamist insurgents.