RMC Sport reported that Aboukhlal had a run-in with Toulouse's deputy mayor in charge of sports, Laurence Arribage, at a ceremony to celebrate the club's French Cup final victory against Nantes.
Arribage told RMC Sport the incident had been blown out of proportion, after she had asked the players to keep quiet during the ceremony.
"The players do not like being told to keep quiet like this," Arribage told the French multimedia outlet.
Toulouse said in a statement: "In response to the serious allegations published by RMC Sport against Toulouse Football Club player Zakaria Aboukhlal, the club has announced that the player will train away from the professional squad until further notice, pending the results of an internal investigation."
Aboukhlal was one of the Toulouse players who refused to take part in a league-wide campaign against homophobia, transphobia and biphobia last weekend.
The Morocco defender defended his choice not to take part in the campaign.
"Respect is a value that I hold in great esteem. It extends to others, but it also encompasses respect for my own personal beliefs. Hence, I don't believe I am the most suitable person to participate in this campaign," he wrote on Twitter.
Nantes forward Mostafa Mohamed also refused to take part, saying on Twitter on Monday: "Given my roots, my culture, the importance of my convictions and beliefs, it was not possible for me to participate in this campaign."
The Egypt international was fined by the club, Nantes said.
