A group of football officials led by Ashfaq Hussain, which was elected by the Supreme Court in 2018 to run the PFF but was not recognised by FIFA, took over the headquarters recently and seized control from the FIFA Normalisation Committee headed by Haroon Malik, local media reported.
FIFA said in Wednesday's statement that its decision to suspend the PFF was prompted by the "hostile takeover" which constituted a serious violation of its statutes.
"FIFA issued a letter warning that, should the illegitimate occupation of the PFF headquarters not be lifted and the office bearers recognised by FIFA not be permitted free access to the building to carry out their mandate, the matter would be immediately submitted to the Bureau of the Council for decision," FIFA said.
"As the situation remains unchanged, the Bureau of the Council has decided to suspend the PFF."
Pakistan was also suspended by FIFA for third party interference in 2017.
The Chadian Ministry of Youth and Sports had stripped the country's FA of its powers on March 10 following concerns over the way it was being run and a breakdown in communication. Last month the country was disqualified from the Africa Cup of Nations by the Confederation of African Football due to the interference.