MP George Galloway has said an activist from his anti-war Respect party was wrong to urge Muslims in east London to stop co-operating with police.
He told BBC One's Question Time that Yvonne Ridley's suggestion - made after a raid in which a terror suspect was shot - was "not our policy".
However, he said "angry young Muslims" were already withholding assistance.
This was because they had seen fellow Muslims "shot, then slandered" by the Metropolitan Police, he claimed.
"Our policy is not that we should withdraw co-operation from the police," Mr Galloway said.
"But you'll be fooling yourself if you think that this feeling of no confidence in the police in London is not the prevalent feeling amongst - especially - young Muslims."
This was "after a series of events that I characterise as 'SAS' - shoot and slander," he added.
"People are shot down by the police and then they're slandered by the police afterwards in an attempt to confuse people about the blunders that have been made."
'Islamophobia in police'
Ms Ridley became a Muslim after being arrested by the Taleban in Afghanistan five years ago.
She told a meeting of the Newham branch of the Respect Party on Tuesday that Muslims should "boycott the police and refuse to co-operate with them in any way, shape or form".
She said this applied to anything "from asking the community copper for directions to passing the time of day with a beat officer".
Ms Ridley was formerly a journalist for the Sunday Express newspaper
Ms Ridley told BBC News this was because the Metropolitan Police had "demonstrated time and time again its Islamophobic attitudes".
Later she clarified her remarks, saying she only wanted Muslim leaders to stop co-operating, not the whole community.
The two brothers arrested are being held at London's high-security Paddington Green police station.
Police have until 1600 BST on Saturday to question them under the terms of their present warrant, but they can apply for this to be extended until up to 14 days after the time of their arrest.
Scotland Yard Assistant Commissioner Andy Hayman said on Thursday he regretted the disruption caused to the community in Forest Gate but that police had to act on intelligence received.
Mr Hayman said they would continue "to try and bottom it out" and indicated officers would meet the local community to reflect on their tactics.
Police have yet to find what specific intelligence suggested they would in the house - reportedly a chemical-based explosive device.
But Mr Hayman said the investigation was continuing and if police did not find it there, the search could go on elsewhere to prove or disprove the intelligence.
Andy Hayman apologised for any disruption caused by the raid
The assistant commissioner said there had been "a time of reflection" since the raid.
"I am aware that in mounting this operation we have caused disruption and inconvenience to many residents in Newham and for that I apologise," he said.
Mr Hayman said he understood that some communities "may be feeling confused or indeed, angry", but he insisted anti-terror operations were not targeted against any particular community or section of a community.
"We are working tirelessly to target criminals who are intent on spreading fear and terror amongst us all."