Police deny relations with the community have deteriorated.
The North West Counter Terrorism Unit carried out an investigation which involved officers posing as Muslims.
They attended prayer meetings and services at a dozen unnamed mosques in Manchester after they befriended four Muslim men for more than a year.
Three of the men, Munir Farooqi, 54, Israr Malik, 24, and Matthew Newton, 29, were convicted of terrorism charges in September. Another man was acquitted.
The court heard Farooqi, a former Taliban fighter, had tried to recruit the undercover policemen to go to Afghanistan to fight British soldiers.
Malik and Newton worked alongside Farooqi at his bookstall.
Farooqi was given four life sentences, Newton was jailed for six years and Malik was given an indeterminate sentence and told he would serve at least five years.
But the covert nature of the operation has led to tensions between Greater Manchester Police and its Islamic advisory group.
Yasmin Dar, a member of the Greater Manchester Police (GMP) Mosques and Community Forum, said: "It's alarming, you've got one community that is being targeted.
"I've not heard of any cases of undercover officers going into churches or synagogues, so why a particular faith? Relations with the police have hit rock bottom. It's created a lot of mistrust with the police."
Another Forum member Rabnawaz Akbar said: "Mosques are a special place for Muslims and when people were told that this had happened they just felt betrayed. It's left a scar on the good relations that had been built over the years."
Ms Dar said this issue, coupled with the police decision to apply to confiscate the home where Farooqi's family live led to all 15 members of the forum walking out of a meeting with the police earlier this month.
At the meeting they had called on the Chief Constable Peter Fahy to reconsider the decision to apply to court for a forfeiture order.
The Muslim Safety Forum, a national organisation which advises the police on issues concerning British Muslims, says the way in which counter terror investigations are carried out must change.
However, Professor Eric Grove, from the Centre for International Security and War Studies at the University of Salford, believes that undercover investigations are necessary, including possible conversions to Islam.
'Part of counter terrorism'
"I don't think there's much alternative to the current tactics, in the current circumstances. Human intelligence infiltrating the society from which terrorists, sadly, do come, is a necessary part of any counter terrorism campaign.
"If people are converting for this, you can see why imams find this difficult and unwelcome, but on the other hand it's probably inevitable."
Imam Habib-ur-Rehman, of the Madina Mosque in Levenshulme, says that he feels insulted by the fact that non-Muslims pretended to be part of the faith.
He said: "We will never welcome such people who record our messages secretly, not such undercover activities, definitely not. We will never support them."
Nomi Khan Worshipper at Manchester Central MosqueI support the police, and I'm against terrorism, but this gives mosques, Muslims and the police a bad name.”
The Muslim Safety Forum (MSF) represents more than 30 Islamic organisations including the Muslim Council of Britain, Muslim Parliament, Federation of Student Islamic Societies, and mosques.
It offers advice to the Metropolitan Police and Association of Chief Police Officers (ACPO) on Islamic issues. Its counter terrorism spokesman Shamiul Joarder argues Muslims are already taking the lead in the fight against extremism.
"We've seen it through Finsbury Park Mosque - it was the Muslims who took out Abu Hamza."
He says the authorities need the support of the Muslim community in order to counter terrorist activity effectively.
"The police haven't managed to foster positive relationships with the Muslim community, otherwise they could use these channels to get the information they need. This kind of infiltration is not the way forward."
'Praised by the judge'
Greater Manchester Police declined to give an interview but issued a statement. It said: "There was simply no other way for this terror network to be uncovered other than the use of undercover officers, and the police were praised by the judge.
"We also do not agree with the view that relations with the Muslim community are at an all-time low - that does not reflect the numerous consultations, forums and public meetings we have had with members of the community since the convictions.
"We accept the forfeiture order is an emotive one and has engendered strong feelings, but the response we had to the convictions themselves was very positive."