"They have been suspended by the national federation until further notice," FTF general manager Zepp Akuete told state radio.
Adebayor, who scored twice in Togo's 3-1 weekend victory over Sierra Leone in Lome, has said he was considering his international future after receiving death threats when he threatened to boycott Saturday's African Nations Cup qualifier.
The two other players suspended are forward Mohamed Kader Coubadja and defender Nibombe Dare. All three are demanding payments they claim are still outstanding after Togo qualified for the first time for the World Cup finals last year.
According to the FTF, the three players want a further 30 million CFA francs (31,000 pounds) on top of the 50 million CFA francs they have already been paid. The federation says it does not have any additional funds to pay them.
The Togolese press reported on Monday that the FTF was suspending the players because of the intransigence and hostility they had shown in a meeting before the match on Saturday.
Akuete said the suspensions could be lifted if the players apologised.