FIFA said in a statement that the suspension would prevent Pakistani teams, including the national side, from playing in international competition and the PFF from benefiting from FIFA development and training programmes.
"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," said FIFA.
"The suspension will be lifted once the PFF offices and access to the PFF accounts are returned to the PFF."
Pakistan's football federation (PFF) has been engulfed in chaos and split into two warring factions following a tussle for the presidency in 2015.
Then-PFF president Makhdoom Syed Faisal Saleh Hayat was accused of embezzlement by the second faction, which had the backing of an influential figure in the ruling Pakistan Muslim League-Nawaz (PML-N) party. Hayat denies any wrongdoing.
The matter has been in the courts in recent years and judges have appointed an administrator to temporarily oversee the federation, which has been dogged by incompetence allegations and claims of corruption.
Acting Secretary of PFF, Syed Farasat Ali Shah, told Reuters the football body will hold fresh elections once the court's proceedings are over.
"Pakistan's football is in a difficult situation as there is no chairman or head of PFF. We are consulting the stake-holders to evolve future strategy after FIFA's decision," Shah said.
"Once a new government body of PFF is elected, we will be in a better position to take care of the issue," he added.
In a statement sent to Reuters, Shahid Khokhar, an ally of Hayat, lay the blame for PFF's trouble at the feet of Muhammad Safdar, senior PML-N lawmaker and the son-in-law of recently ousted Pakistani Prime Minister Nawaz Sharif.
According to FIFA records, Pakistan, 200th of 211 teams in the world rankings, have not played a full international since a 0-0 draw with Yemen in a World Cup qualifier in March 2015.
Pakistan have never qualified for the World Cup.
(Writing by Brian Homewood, Drazen Jorgic; Editing by Peter Rutherford and Christian Radnedge)
