Mbappe has not represented his country in the UEFA Nations League during this month's international break, as the Real Madrid star is nursing a thigh strain.
The 25-year-old was pictured outside of a nightclub in the Swedish capital of Stockholm last Thursday, and reports on Monday have since emerged claiming that police responded to an accusation of rape at The Bank Hotel where Mbappe stayed.
Reports from Sweden claim Mbappe is now at the centre of the investigation and is 'reasonably suspected' of rape and sexual molestation.
Real Madrid allegedly held a 'crisis meeting' on Monday, but Mbappe has taken to social media to publicly defended himself and has described the allegation as "fake news", while the player's entourage have described the reports as a "new defamatory rumour".
Without the presence of Mbappe, France beat Belgium 2-1 away from home in the Nations League on Monday evening, and after the match, manager Deschamps addressed the allegations against his captain.
Deschamps addresses Mbappe rape allegations
"Everyone is free to write what they want but there is a negative atmosphere," Deschamps told reporters.
"Be careful when you pick things up. You had better take a bit of a step back before publishing anything and everything, but these things happen so often.
"There are things that are not difficult to verify, but if you credit any old thing... In any case I am not going to talk to him about it. He is big enough to know how to communicate."
Meanwhile, Mbappe is scheduled to attend a hearing at the Ligue de Football Professionnel's appeal committee on Tuesday over £46m in unpaid wages he is disputably owed by former club Paris Saint-Germain.
Mbappe spent seven years at PSG and departed as their all-time record goalscorer upon the expiration of his contract in the summer in order to complete a free transfer to Real Madrid.
The forward has since scored seven goals in 11 appearances for the Spanish giants across all competitions and he is planning to build up his match fitness ahead of returning to Carlos Ancelotti's side after the international break.