Opinion remains divided after two brothers arrested by anti-terrorist police in a raid on a house in east London were released without charge.
Mohammed Abdul Kahar was shot during the raid
Home Secretary John Reid said police had been acting in the interests of the community after they received intelligence about a suspected chemical device and the Muslim Council of Britain said it hoped "lessons would be learned".
Some Muslim leaders suggested already strained community relations could be damaged further.
Mohammed Abdulkahar, 23, was treated in hospital for a wounded shoulder after being shot in the raid in Forest Gate on 2 June.
In a statement, Mr Reid said police had been working to protect the whole community.
"They therefore deserve the support of the whole community in doing what is often a very hazardous and dangerous job often involving difficult decisions," he said.
Damian Hockney, a member of the Metropolitan Police Authority, which oversees the London police force, said the incident was embarrassing but officers had been in an "impossible" position.
"They could not ignore the issue and this is not a signal to lower our
guard," he said.
"There is a threat to London and the Met have been successful on many occasions in thwarting potential terrorist operations.
"They need our support for this job and I believe that most people in Forest
Gate fully understand this."
Commander Rose Fitzpatrick of the Metropolitan Police, meanwhile, told BBC's Newsnight "the community thinks that we could have told them a little more earlier".
She added: "We've explained to them that we always need to balance our intelligence, our need for public safety and I think what we can do in future is make sure that people understand what we can tell them, when we can tell them and why we can't."
Police and intelligence services were criticised by the Islamic Human Rights Commission.
"This is another indictment of police and intelligence service anti-terrorist policy," said IHRC chairman Massoud Shadjareh.
"This policy is criminalising and victimising a community that is running out of patience.
"The only criteria for suspicion it appears is the suspicion that you might be or are a Muslim."
The Muslim Council of Britain welcomed the men's release and said it hoped "appropriate lessons will be learned".
MCB Secretary-General Dr Muhammad Abdul Bari said: "This is not a matter of apportioning blame, but of trying to ensure that the necessary foundations are in place to maintain trust and build a genuine partnership between the Muslim community and the police to defeat a terror threat that looks as if it will be with us for some years to come."
Before the brothers were released, about 100 people had attended a protest outside Forest Gate police station claiming the raid had been symptomatic of oppression of the Islamic community
Asghar Bukhari from the Muslim Public Affairs Committee said the protest capitalised on the police action and did not have the support of the brothers' family.
But he said many more people could be expected to be at a future demonstration organised by the mainstream Muslim community.
"Because of this breakdown in trust you then see Muslims getting far more agitated and angry," he said.
"The Muslim community - remember this isn't the first house that's been raided, hundreds of houses have been raided - are feeling that they no longer trust the intelligence," he said.
"And they are not sure about the police - the police is being far too aggressive, perhaps intimidatory - and that perception is pervading through the Muslim community."