Erik ten Hag claims Cristiano Ronaldo "will not accept" his charge from the Football Association.
Ronaldo had until Monday to respond to the FA over his charge of alleged improper conduct.
The FA charged the Manchester United forward with a breach of FA Rule R3 for an incident that took place after their defeat at Everton on April 9.
Read more: Why Harry Maguire was in the United dressing room vs Everton
The FA said "it is alleged that the forward's conduct after the final whistle was improper and/or violent".
Ronaldo was filmed knocking a fan's phone to the floor as United players approached the away dressing room following the 1-0 loss.
"We spoke about that, he will not accept it," Ten Hag said.
It is understood Ronaldo will defend himself in any hearing and the club and manager are supporting him over the matter. He may not contest the charge but will defend himself vigorously.
Merseyside police confirmed on August 17 that Ronaldo, 37, had been cautioned after they interviewed him in relation to an allegation of assault and criminal damage.
The force said in a statement: “We can confirm that a 37-year-old man voluntarily attended and was interviewed under caution in relation to an allegation of assault and criminal damage.
“The allegation relates to an incident following the Everton v Manchester United football match at Goodison Park on Saturday 9 April.
“The matter has been dealt with by way of conditional caution. The matter has now concluded.”
United are believed to be baffled the FA has charged Ronaldo nearly six months after the incident and a month after the police concluded their investigation.
Ronaldo returned to Everton on Sunday to emerge and score United's winning goal for his first club goal from open play since April.
The Portugal international is likely to start in the return leg against Omonia Nicosia on Thursday night and Ten Hag downplayed accusations from some former United players, including Rio Ferdinand, Ronaldo had been "disrespected" this season.
"I want to support him as good as possible," Ten Hag explained. "So we have a certain demand on players, what we expect from him in certain positions on the pitch and what I do is I want to get the best player.
"He is getting in better shape now, I am happy with that, he can contribute more to the squad and I'm sure he will do.
"In the start, it was definitely the case (that he was undercooked) and it's proven once again no one can miss pre-season because of the after-effects."
READ MORE:
