The world governing body said on Wednesday that Pakistan's national and club teams are not entitled to take part in international competitions until the suspension is lifted.
"The Bureau [of the FIFA Council] took this decision as a result of the fact that the PFF offices and its accounts remain in control of a court-appointed administrator, which constitutes a violation of the PFF obligations to manage its affairs independently and without influence from any third parties in accordance with the FIFA Statutes," FIFA said in a statement.
It added, "The suspension will be lifted once the PFF offices and access to the PFF accounts are returned to the PFF."
The PFF has now lost all its membership rights as defined in Article 13 of the FIFA Statutes.
The suspension also means that neither the PFF nor any of its members or officials can benefit from any development programs, courses or training from FIFA or the Asian Football Confederation (AFC).
Furthermore, other member associations may not entertain sporting contact with the PFF during its suspension as stated in Article 16 of Paragraph 3 of the FIFA Statutes.
The election of former federal minister and Pakistan Peoples Party (PPP) leader Syed Faisal Saleh Hayat as President of PFF in a controversial election in June 2015 effectively led to a stoppage in the running of football in Pakistan.
According to FIFA records, Pakistan, which stands 200th in the world rankings, has not played a full international since a 0-0 draw with Yemen in a World Cup qualifier in March 2015.
Pakistan has never won a ticket for the quadrennial international football tournament.