Doherty will have to isolate until the middle of next week, ruling him out of Saturday's Premier League match against Manchester City and potentially the Europa League visit of Ludogorets on Thursday.
Mourinho has already taken aim at Wales and England in the past fortnight and he renewed his assault on international football, saying he was doubtful federations were following Uefa’s Covid protocols to the letter.
Asked about Doherty's situation, Mourinho said: "I can speak about my club and I can have the feeling that the other clubs also work extremely well around this problem that we all have.
"When the players leave the club bubble, the story is a different story.
"I have my doubts if everybody follows protocols in the way where the player is protected, a position is protected and society is protected too. I have my doubts.
"It is a bit difficult for me to understand that the player, after a game, in the same night of the game, has a positive result.
"Why after? Why not before? It's a simple question, probably with a simple answer, but I don't have the answer.
"Matt is ok. Of course he's isolated even from his family, his wife, his two little children. He is isolated, we are taking care of him medically – nutritionist, sports science – and now he feels good but we have to follow protocols so normally after a negative test next week he should be back."
Speaking on his one-year anniversary as Spurs boss, Mourinho claimed he was even happier now than when he took the job and said he was hopeful of being of still being in charge in another year’s time.
"The more empathy, the more connection with the people you work with, the happier you are and the happier you are, the more you can give," Mourinho said.
"And in my case now, I can say that one year after, I am even happier than when I was when I got the job and I came, so that for me is a very good feeling.
"You ask me now ‘do you see yourself here in one year’s time?’ Of course I do because I’m very happy here.”
Spurs can return to the top of the table with a win over Manchester City in north London on Saturday.
Mourinho's critics have claimed he is yesterday's man but he insisted he is only improving with age and new experiences.
“I keep saying that our job is the kind where if the passion stays there, you can only get better," he said.
"Because it’s a job where the accumulation of experiences can only make you better.
"And, for me, it was not just an accumulation of experiences but also new experiences. Coming to a club mid-season was the second time in 20 years of football.
"The lockdown, the Covid, of course, was the first time. To work very hard and to admire the work my club did, doing a wise, balanced [transfer] market in such a difficult moment, was also a great experience.
"To create that mentality of the next game we want to win looks a simple thing, looks basic but it’s not basic. It’s very difficult, the next game we want to win. We are going to lose, I keep saying the same, we are going to draw. But the mentality of the next game, I want to win."
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