According to reports, the midfielder was not allowed to train with his teammates on Thursday, with the former Paris Saint-Germain man advised he had been suspended by the club for a week.
However, there has been no official reason given by the Ligue 1 club, who just instead released a short statement saying the player, who was made available for transfer in the summer, is not currently being considered for selection by boss Paulo Sousa.
It has been claimed Sankhare only became aware of the development on Thursday after he was unable to access the club car park and locker rooms when he turned up for training.
The 29-year-old was expected to leave over the summer and, along with first-team squad members Thomas Carrique, Paul Baysse and Jonathan Cafu, was put on the transfer list, but he could not secure a move away before the window closed on Monday.
The reports claim Carrique, Bayasse and Cafu have all been training as normal but Sankhare has been suspended.
Sankhare, a former France youth player up to Under-21 level, is now a full Senegal international and has played 84 times in all competitions for Bordeaux, scoring 19 goals since making his debut for the club in February 2017.
It appears likely the midfielder will seek a move away in January when the transfer window reopens and it would be a major surprise if he plays for the club again following the latest development.
Bordeaux have won just one of their first four Ligue 1 games this season and sit 11th in the table. They take on Metz at home when the domestic action resumes on September 14.