The 2010 agreement aimed to facilitate the return of Pakistani illegal immigrants and other nationals who had transited through Pakistan before arriving in the EU.
Interior Minister Chaudhry Nisar Ali Khan said European countries were misusing the agreement.
“Pakistanis travelling illegally to any Western country are to be deported after proper verification” of their nationality and other relevant details from Pakistan, state-run Radio Pakistan quoted Khan as telling local media in Islamabad.
But, he said, “most of the (Western) countries are deporting people without verification by Pakistani authorities”.
Khan said 90,000 people were sent back to Pakistan from various countries last year alone.
“Another dangerous trend has emerged for the last several months under which Pakistanis travelling abroad without documents are deported on charges of terrorism without verification whether or not they are actually Pakistanis,” he said.
The minister did not say when the agreement was suspended or name any country which had recently deported Pakistanis on charges of terrorism.
European Union delegation officials contacted in Islamabad expressed ignorance of the move.
“We are not aware of any such development,” an EU official told AFP on condition of anonymity.
The announcement came two days after Greek police arrested 12 members of a gang including nine Pakistanis that forged documents for migrants trying to reach central Europe.
Around 630,000 people have illegally entered the European Union this year, more than half of them landing in Greece, and the bloc has struggled to formulate a strategy to deal with the crisis.
Analysts said Islamabad’s move would only create more problems for Pakistanis staying illegally in EU countries.
“The statement is uncalled for as it will add to the miseries of Pakistanis who illegally enter European countries,” political analyst Hasan Askari told AFP.
He said asking EU countries for verification of nationality and other details of illegal entrants would mean they would be held in jail until Pakistani authorities completed the verification process.