David Cameron's renewed crackdown on British-born extremists will push marginalised young people further towards radicalisation, the UK's biggest Muslim organisation has said.

Harun Khan, deputy secretary general of the Muslim Council of Britain (MCB), raised concerns about the prime minister's anti-terrorism strategy amid signs of a wider impasse in relations between the government and Muslim groups.

"They need to be talking to us and others to understand what it is that's leading these boys down this route," Khan told the Guardian. "Part of the problem is the constant talk of legislation, harassment and monitoring, stripping people of their passports. This is what's leading young people towards radicalism."

The warning came as Cameron and Nick Clegg held further talks to try to agree on the final details of plans to stem the flow of British-born jihadis travelling to and from Syria and Iraq. Cameron is due to make a statement to MPs at 3.30pm on the proposals, which are expected to include measures to improve the flow of information about airline passengers to intelligence agencies and to intensify cooperation with Germany and Turkey, the main routes to Syria.

Khan said many young British-born Muslims felt pushed to the fringes of society and that the latest government crackdown could nudge them further into the grasp of radical clerics, instead of drawing them back into mainstream society.

"This is really unprecedented in what we're seeing right now with young people," he said. "People are watching the news and thinking: 'These people are getting slaughtered, I need to do something'. Now we've put all these people out of the country and we're saying you can't come back in."

That warning was reinforced by the managing director of the Quillam Foundation thinktank, Ghaffar Hussain, who said the government had a counter-terror strategy, but not a counter-extremism one.

"The problem is the government's policy seems to be once people get radicalised then we will try stop them, but once someone is radicalised it's too late – you've lost them," he said. "The key is stopping them before they are radicalised."

Khan said the MCB, which represents more than 500 mosques and Muslim groups, had a constructive relationship with the previous Labour government, but it had been "very difficult to have any formal engagement at all" since the coalition came to power.

"Just some level of dialogue and discussion would help if we're going to address the issues around extremism," he said.

Saleem Kidwai, the secretary general of the Muslim Council of Wales, urged the Home Office to re-open its dialogue with the MCB, saying the impasse could foster a mutual distrust between the government and community groups.

"I would say to the government, you must talk to the Muslim Council of Britain because it is the largest organisation. You can talk to thinktanks but they are not the grassroots groups – the MCB has got the mandate from 500 organisations who represent Muslims from all walks of life. I know they would love to help rather than obstruct."