Help will also be given to break down barriers facing private faith schools that want to switch to the state sector, ministers said, with extra cash made available to improve facilities if schools do not have the money.
The backing came in a document, Faith in the System, released jointly by the Department for Children, Schools and Families and leaders of faith groups.
The document coincides with a duty on schools to promote community cohesion. Ed Balls, Secretary of State for Children, Schools and Families, said faith schools had a central role to play in producing better community relations.
"I'm keen to work with all faith communities to drive up standards and promote cohesion," he said.
But the document sparked criticism from teachers' leaders and secularists, who said the schools were divisive. New research also casts doubt on whether religious secondary schools in London serve disadvantaged pupils.
Mary Bousted, general secretary of the Association of Teachers and Lecturers, said the admissions policies and curriculum of many faith schools did not promote equality.
"Our members believe that we need schools which embrace the diversity within our community, not a diversity of schools dividing pupils and staff on religious grounds," she said.
The faith schools document highlights a particular shortage of school places for Muslim, Sikh and Hindu pupils. The last census showed that there were 376,000 Muslim children aged between 5 and 15, but only 1,770 pupils in seven state-funded Muslim schools in England.
There are 115 private Muslim schools that could get state funding if they win backing from their communities and meet requirements on the national curriculum and employment law.
"We recognise that there are nearly 15,000 Muslim children and around 11,000 Jewish children whose parents choose to send them to independent schools with a particular religious character," the document said. "The availability of places in the maintained sector could provide an important contribution to integration and empowerment of these communities."
The launch of Faith in the System allowed ministers to present a united front with faith schools after a battle last year over admission quotas. Alan Johnson, the former education secretary, wanted new faith schools to offer guaranteed places to children of a different faith or none but was forced into an embarrassing U-turn.
All new faith academies will be expected to offer at least half of their places to pupils of other faiths or none, the document said. The Church of England said it is in discussions with a Muslim organisation in Oldham to open the first joint faith school. It is expected to be one of three new academies in the city.
The Hindu Council UK, which backed the document, said multi-faith schools were better than single-faith ones at teaching pupils about religion in a balanced way.
John Dunford, general secretary of the Association of School and College Leaders, said the next step should be to establish a national curriculum for RE to give pupils a common understanding of faith.
Mr Balls said Building Schools for the Future, the secondary rebuilding programme, would make it easier for local authorities to plan for new faith schools and give them the money to build them. He said the Government did not have a view on how many faith schools there should be and that such decisions had to be made locally, depending on parents' wishes.
But research published this week casts doubt on claims by faith-school leaders that they are serving all sections of society. Rebecca Allen, of London University's Institute of Education, and Anne West, of the London School of Economics, said religious secondaries in London do not serve the most disadvantaged pupils.
"Overall, religious schools educate a much smaller proportion of pupils eligible for free school meals and their intakes are significantly more affluent than the neighbourhood they are located in," they said.
"Some London religious schools may have undergone a distortion of mission as happened with elite public schools, which were set up to educate the poor but then shifted their focus and catered predominantly for the wealthy."
Mr Balls said there was more to do to ensure that no schools discouraged poorer pupils from applying. Faith schools backed the new admissions code, which bans interviews and questions about parental background, he said.
Where ethos is a religion
A third of all maintained schools are faith schools
There are approximately 6,850 faith schools from a total of nearly 21,000
Around 600 of the faith schools are secondaries. The majority of faith schools are Church of England and Roman Catholic
There are 37 Jewish schools, seven Muslim, two Sikh, one Greek Orthodox and one Seventh Day Adventist
Of the 83 academies now open, 27 have a faith designation
25 per cent of places in new Church of England schools are for children of other faiths or none.