The government is planning to intervene in some mosques to support Muslims who want to marginalise extremists.
Communities Secretary Ruth Kelly will announce a new role for the Charity Commission, strengthening its task of overseeing religious institutions.
A £600,000 faith unit within the commission will help Muslims strengthen governance and leadership in mosques.
Ministers are also changing how prosecutors target extremists, with new specialist counter-terrorism teams.
The plans are part of the government's broader counter-terrorism strategy.
In February, ministers announced support for pilot projects to root out
Islamist extremists grooming young men in British cities.
Ruth Kelly: Meeting more Muslim groups
In a speech on Thursday, Ruth Kelly is expected to say: "I do not under-estimate the difficulties we face or the scale of this challenge. But I know from my conversations with Muslim communities up and down the country that the desire and commitment to tackle extremism is there.
"Success will hinge on forging a new alliance against violent extremism. We need to reach out and give greater support to the overwhelming majority who are disgusted by terrorist attacks carried out in the name of Islam."
Ms Kelly's department has changed government strategy by launching talks with a broader range of Muslim groups.
But at the same time, the largest body, the Muslim Council of Britain, has fallen out of favour, leading to claims that ministers are talking only to those prepared to agree with government.
In a related move, the Attorney General Lord Goldsmith said specialist prosecutors are beginning to work with police officers to improve how they target extremist preachers.
"For some time I have been concerned that we have not taken sufficiently effective action against a very small minority of extremists among our communities who incite others to terrorism," said Lord Goldsmith.
"By bringing together the law enforcement agencies and the prosecutors we now have a commitment to tackle these cases in an effective, focused and well co-ordinated way and the structures to enable that to happen."
The strategy is part of the government's attempts to develop a plan to prevent extremism, a key plank of counter-terrorism policy.
New research commissioned by the government links radicalisation of young Muslims with a failure of traditional mosque leadership.
The study, written by a Muslim academic, is understood to pinpoint a conveyor belt towards extremism which starts with identity crises during teenager years. These problems are then easily compounded by discrimination, lack of opportunity and the poor quality of religious leadership in some traditional mosques.
The BBC understands the research warns the government that extremist groups successfully recruit by exploiting a combination of alienation and religious illiteracy among youths.
But at the same time, the report predicts that a positive British-Islam voice can emerge to defeat extremists, if there is investment in religious leadership.