Well-known British hard-line Muslim, Abu Izzadeen, called out during Mr Reid’s speech calling him an enemy of Islam and Muslims.
"Shame on us," the bearded, white-robed Izzadeen said, in reference to other Muslims attending the address in an east London district where there’s a large Islamic population.
Mr Izzadeen refused to be ejected by security guards as he interrupted the address, Mr Reid's first to a Muslim audience since becoming home secretary in May.
Speaking at an east London school, Mr Reid emphasised the need for greater parental responsibility to help stem the radicalisation of young Muslims into “home-grown” militants.
The event was billed as an attempt to engage with Muslims over the issues at the heart of security concerns gripping the country.
Reid calls for vigilance
Mr Reid urged moderate Muslims to be constantly on the lookout for extremists.
"These fanatics are looking to groom and brainwash children, including your children, for suicide bombing, to kill themselves in order to murder others," he said.
"Look for the tell-tale signs now and talk to them before their hatred grows and you risk losing them forever. In protecting our families, we are protecting our community."
The father of two boys acknowledged the difficulties in raising children and keeping tabs on them at all times.
"I know how hard it is, sometimes, to see what is in front of our eyes, particularly when it is something that we do not agree with," he said.
"But there are some circumstances when we need to intervene, when we need to challenge or confront their behaviour in order to protect them from others and to protect them from harm."
Fight against radicalisation
London has been on high alert ever since a multiple terrorist attack in July 2005 which left 56 people dead including four British suicide bombers.
The men were apparently radicalised at local Muslim communities, sparking fears of a “home-grown” terrorist threat.
Since the 2005 bombings, the ensuing security clampdown has led to many arrests.
But there have also been a number of high-profile cases in which police staged raids on Muslim suspects but ultimately let them go for lack of evidence.
Muslim groups have responded angrily and said there’s a perception that police are disproportionately targeting the community, particularly already-marginalised young men.
Mr Reid has repeatedly defended the crackdowns.
Accusations of spy request
Mr Reid was largely unfazed by the heckling, responded to the protests at his speech calmly.
When a second protestor was finally ejected Mr Reid said he would have preferred them to stay, to engage in a "dialogue" with them.
His address came a day after Mr Reid wrote an article in The Sun tabloid suggesting the Islamic community should hand their sons to police if they suspect them of being involved in terrorism.
That prompted Ahmed Versi, the editor of the Muslim News newspaper, to accuse Mr Reid of asking the community to "spy" on their sons.
The British government has made efforts to involve the country's 1.5 million Muslims in the fight against extremism after the September 11, 2001 attacks in the United States.
Memorial of British victims
Meanwhile Mr Reid also attended a national memorial service remembering the British victims of bombings in Egypt, Turkey and Qatar on Wednesday.
One father called on Prime Minister Tony Blair to do more to help victims of terrorist attacks abroad.
Mr Blair, Mr Reid, and Culture Secretary Tessa Jowell joined relatives for the service at London's Southwark Cathedral to commemorate the 13 British victims of the Sharm-el-Sheik, Kusadasi and Doha bombings last year.