Injuries have also hampered the progress of the 27-year-old, who was expected to challenge the likes of Juan Mata for a spot in the starting line-up.
"I think it takes time," Mourinho told reporters on Friday. "Some players, their profile is adapted to come and play, some others they need more time to feel the intensity and the aggression, the game without the ball, the competitiveness.
"Micky needs time to become the top player he can be. Of course we believe in him and of course we believe that sooner or later there will be no problem."
Mourinho, who said Mkhitaryan was training with the team "100 percent with no limitation" will be looking for his side to bounce back when they host 14th-placed Burnley on Saturday.
After a strong start to the Premier League with three successive wins, Mourinho's side have endured a stop-start campaign.
And last weekend's 4-0 humiliation at the hands of Chelsea leaving them six points behind leaders Manchester City in the standings.
"We are a team in process, we are a team in the process of building up," Mourinho said.
"You don't do that with one transfer window, you don't do that in three or four months but in this moment we just think about game by game, and now it is Burnley and Burnley is difficult, I know that."
Mourinho said a congested fixture list would make Saturday's clash against Sean Dyche's side a tougher challenge than usual.
"Liverpool two days, Fenerbahce two days (off), Chelsea, two days, (Man) City two days, Burnley now," he said, of his side's run of six matches in 13 days.
"And finally we are going to have a Sunday off and a little bit of time till the next Fenerbahce match, so I am waiting for a very difficult match against Burnley."
(Reporting by Nivedita Shankar in Bengaluru, editing by Simon Cambers)
