Authorities have moved to force overseas-funded aid organisations to re-register under stricter rules that came into force two years ago, leading several to lose their licenses.
"We believe that we are one of more than 20 organisations whose registrations have been rejected," Jonathan Birchall, the lead Communications Officer for Open Society Foundations told AFP.
The organisation, which is funded by the US billionaire philanthropist George Soros and runs a raft of programmes from education to governance, had earlier issued a statement seeking clarification from the interior ministry over the move.
International charity ActionAid, which supports a range of projects from livelihoods to women's rights, has also said it is being forced to leave Pakistan.
The organisation "has been given 60 days to close all operations in the country", it said in a statement released last week, after its application to register under Pakistan's new rules for international non-governmental organisations was declined.
Pakistan officials declined to comment when contacted by AFP.
While terrorism and natural disasters plague parts of Pakistan, the country has shown increasing suspicion of foreign aid groups in recent years.
In 2012, a Pakistan intelligence report linked the aid group Save the Children to the doctor, Shakeel Afridi, who the CIA used to carry out a fake vaccination programme as they searched for Al-Qaeda chief Osama bin Laden.
Save the Children has always denied it had any links with Afridi or the CIA.
But the charity's expat staff were forced to leave Pakistan after the accusations emerged.
Pakistan has since hardened its policies towards international aid groups, accusing them of being covers for spying operations, and has repeatedly warned them to restrict their activities.
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