The world football governing body in a statement on its website following its emergency meeting on Wednesday, issued a deadline extension of a week with Monday 1 September earlier set for the group to vacate office.
Fifa insists they will not recongnise the elective congress held at Chida Hotel, Abuja which produced the Chris Giwa-led executive board.
Fifa ordered that the Aminu Maigari-led NFF board be allowed to supervise fresh elections.
"Following the decision by the FIFA Emergency Committee, FIFA has today, 3 September 2014, sent a letter to the Nigeria Football Federation (NFF) confirming that the NFF will be suspended with immediate effect should there still be persons claiming to have been elected to NFF positions on 26 August 2014 and occupying their offices on Monday, 8 September 2014 at 08.00 (Central European Time)," a statement on its website read.
The decision follows events linked to the NFF general assembly held on 26 August 2014. While the said general assembly was duly convened by the NFF Executive Committee to adopt a new roadmap leading to the NFF elections, some members proceeded to hold elections in the absence of the NFF President, who was being held by security forces for questioning.
"In a letter sent on 29 August 2014, FIFA confirmed that it would not recognise the results of the aforementioned elections and that the matter would be brought to the respective FIFA bodies should there still be persons claiming to have been elected and occupying the NFF offices at midnight on 1 September 2014. On expiry of the deadline, some people were still claiming to have been elected and were occupying the NFF premises.
"Given the current circumstances, the FIFA Emergency Committee has decided to set a new deadline of 8 September 2014 at 08.00 CET. Should the new deadline not be respected, the NFF will be automatically suspended until the board claiming to be elected vacates the premises of the NFF and the NFF General Secretary is able to perform his work without interference.
"The NFF Executive Committee as it was composed on 25 August 2014, meaning under the presidency of Aminu Maigari, should then convene as soon as possible a first extraordinary general assembly to elect the members of the electoral committee and a second extraordinary general assembly in the shortest time possible allowed by law in order to proceed with the elections of new NFF office-bearers," it concluded.
The second NFF faction is set to conduct elections on Thursday, September 4.