A group of officials led by Ashfaq Hussain Shah, which was elected by the Supreme Court in 2018 to run the PFF but was not recognised by FIFA, took over the headquarters in March last year.
They had seized control from FIFA's normalisation committee headed by Haroon Malik, with Shah saying the committee had not conducted elections for the body in the 18 months since it took charge.
FIFA suspended the PFF due to the "hostile takeover" but said it now had confirmation the committee had regained full control of the PFF's premises and was in a position to manage its finances.
"The PFF was also informed that any undue interference in its affairs or action that could hinder the fulfilment of the mandate of the normalisation committee might lead to the PFF being suspended again and/or the imposition of other sanctions provided for in the FIFA Statutes," FIFA added in a statement.
"As the deadline by which the normalisation committee was required to fulfil its mandate (30 June 2022) is now no longer realistic, the Bureau (of the FIFA Council) has also decided to extend the committee's mandate until 30 June 2023 at the latest."
Pakistan was also suspended by FIFA for third party interference in 2017.