Ole Gunnar Solskjaer said the anti-Glazer protest that forced the postponement of Manchester United's clash against Liverpool went "too far" but reiterated his call for supporters' voices to be heard.
Anger at American owners the Glazers, who took charge of the club in 2005, spiked after their recent attempt to join the breakaway European Super League.
Thousands of protestors descended on Old Trafford demanding change before Sunday's scheduled Premier League match against arch-rivals Liverpool.
Around 200 fans got into the stadium and invaded the pitch, while another group made their frustrations clear at the team hotel in Manchester.
Solskjaer, speaking on Wednesday for the first time since the chaotic scenes, said it had been a difficult day for United, who had wanted to beat Liverpool "for the fans".
"That's the players' focus, that's my focus but, as I said before the game, we have to listen," he said ahead of Thursday's second leg of his side's Europa League semi-final with Roma in Italy.
"We have to hear the fans' voice. It's everyone's right to protest, it has to be in a civilised manner, though. It has to be in a peaceful manner.
"Unfortunately, when you break in, when police officers get injured, scarred for life, that's too far.
"That's one step too far. When it gets out of hand like this, it's a police matter. It's not about showing your opinions anymore."
A police spokesman said on Tuesday that six officers were injured as flares were let off and bottles thrown, with one sustaining a fractured eye socket and another a facial wound.
A 28-year-old man was charged with a number of offences including throwing fireworks and use of threatening behaviour outside the Lowry Hotel.
United, seeking their first silverware since 2017, beat Roma 6-2 in the first leg at home and are almost certain to reach the final, where they will play Arsenal or Villarreal.
Solskjaer, whose team have stumbled four times at the semi-final stage over the past two seasons, said he would maintain a "laser focus on the football", with talk of more protests from angry fans.
"My job, my focus has to be on the results, but you don't really need to be a rocket scientist to see that we have challenges and frictions and things that have to be dealt with within communication," the Norwegian said.
"Other individuals than me of course have started already, discussing with the fans, communicating with fan groups, which is going to be massive for us going forward.
"I think the players have done terrific to be where they are. I would be sad if all the good work the players have done is disrupted, so our focus is on playing well and getting through to a final now."
United co-chairman Joel Glazer has apologised for the Super League debacle saying "we got it wrong".
Asked whether the owners should speak directly to supporters, Solskjaer said: "I've been communicating with the owners. I've got an apology, personally.
"They've apologised to the fans that this came out. I know that there is communication between other individuals than me and the fans."
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