The Hawks nearly boycotted the World Cup in dispute over bonuses
Fifa has ordered the Togo Football Federation (FTF) to hold elections for a new executive by 9 January and review its constitution within three months.
The directives follow a fact-finding mission to the west African country in October by Fifa representative Jan Peeters and Slim Aloulou of Caf.
The TFT, led by Rock Gnassingbe, has been rocked by crisis since four executives members resigned following their disastrous outing at the World Cup in Germany in June.
A difference in opinion with Gnassingbe led the four executives to resign and that prompted Fifa to call for new elections to be supervised by General Seyi Memene, the Togolese vice-president of Caf.
"We have called for the organisation of elections within two months in line with the statutes of 1994 under the supervision of Fifa and Caf and an independent electoral commission chaired by the first CAF vice-president General Seyi Memene," a Fifa spokesman told BBC Sport.
"We have also called for the revision of the Togo FA statutes within three months after these elections with the help of the two Fifa and Caf delegates (Jan Peeters and Slim Aloulou) as well as Fifa legal experts if needed.
"We are convinced that only the proposed road map for the re-organisation of football in Togo can help the federation project in serenity its plans for the future in the unity of the family of Togolese football."
Meanwhile the TFT has welcomed the calls for fresh elections.
"The executive bureau of the Togo Football Federation will remain in office until the elections are held," Lawson Segneame, deputy treasurer of the TFT said.
Togo's maiden World Cup campaign, which ended in the first round, was marred by a dispute between the FTF and its player over bonuses and allowances.
This compelled Fifa to intervene and promise to pay the allowances out of Togo's $5.6 million World Cup appearance fee.