Globally, around 90,000 people were deported back to Pakistan last year for a variety of offences, but in some cases they had been sent back without proper determination they were Pakistan nationals, an interior ministry spokesman said.
It was not immediately clear exactly how many came from Europe, although the figure is in the thousands, he said.
European Union nations signed a deal with Pakistan in 2009 allowing them to repatriate illegal immigrants and other nationalities who transited through Pakistan on their way to Europe.
“There were some irregularities in the implementation of this agreement,” the spokesman, who asked not to be named, said.
“The signing country had to first verify the nationality of that person who was being deported but there were instances where the nationality was not being verified. The minister took notice and the agreement is temporarily suspended.”
EU officials in Pakistan were not immediately available for comment on the Pakistani decision.
Europe is facing its biggest influx of migrants in decades, with many families fleeing war in Syria, Iraq and Afghanistan.
Some European leaders are calling for tighter controls over fears of Islamic State infiltration after attacks in Paris last week killed 127 people and injured around 200.
Pakistan’s refusal to accept deportees could slow down the removal of illegal economic migrants, making it harder to accept those genuinely fleeing persecution.
On Tuesday, Pakistan Interior Minister Chaudhry Nisar said that airlines returning deportees without Pakistani permission would be penalised.
“Any airline that brings deportees to Pakistan without Interior Ministry permission and without Pakistan travel documents will be fined heavily,” he said.
Britain has a separate deal on deportations with Pakistan and is not affected by Tuesday’s decision.
Nisar added that Pakistan would not accept any deportees accused of militant links without clear evidence of guilt.
“Accusing any Pakistani of terrorism without evidence is human rights violation,” he said.
As an example of problems with the system, the interior ministry cited the case of a Pakistani deported from Italy earlier this year who had been accused of militant links.