Phil Woolas, the minister responsible for local government and race relations, said Aishah Azmi, 23, had "put herself in a position where she can't do her job".
Although he told the Sunday Mirror she "should be sacked," he stopped short of repeating his demand yesterday after Ms Azmi's lawyer warned he could influence her employment tribunal case. She has been suspended by the Headfield Church of England Junior School in Dewsbury, West Yorkshire.
Mr Woolas told the BBC's Politics Show: "The headteacher says that she [Ms Azmi] is not able to do her job. I don't think you would want government ministers interfering in individual personnel issues but the general point is clear - if the education can't be provided for children who need it and have a right to it, many of whom are Muslim and other ethnic minority children.
"It's those children that I'm concerned about. And I want them to get the best chance in life as do their parents and they have that right. And if the headteacher says that's the action she needs to be taken, then so be it."
Ms Azmi said pupils had never complained about her wearing a veil. She said she would remove it but not in front of male colleagues. But she admitted she had taken the veil off when she was interviewed for the job by a male governor.
Nick Whittingham, her lawyer, called on Mr Woolas to withdraw his comments. "Mrs Azmi is very well able to carry out her role as a teaching assistant providing support to pupils who speak English as a second language," he said.
Inayat Bunglawala, a spokesman for The Muslim Council of Britain, said: "This remark by Mr Woolas is an outrageous intervention by the Government into a matter that should be decided by the school - and if necessary by the courts."
In a separate row, Nadia Eweida, a Christian British Airways check-in worker, said she had been overwhelmed by messages of support after being, in effect, "forced" to take unpaid leave for refusing to remove or conceal a small cross the size of a 5p piece on a necklace.
She plans to sue the airline, which says that items such as turbans, hijabs and bangles can be openly worn "as it is not practical for staff to conceal them beneath their uniforms".
Peter Hain, the Northern Ireland Secretary, branded BA's ruling "loopy", while Ann Widdecombe, the Tory MP, said she would boycott the airline until it reversed its decision. Muslim leaders backed Miss Eweida's right to wear the cross.
It emerged yesterday the Government aims to allay fears about "parallel societies" developing in Britain by forcing faith schools, including Muslim ones, to admit up to 25 per cent of pupils from other faiths. The Church of England has already agreed to that.
Under plans to be announced this week, education authorities will be allowed to order faith schools to admit up to a quarter of pupils from other religions. If the authority does not make such a request, an individual can ask the Education Secretary to intervene.
David Davis, the Tories' shadow Home Secretary, accused Muslim leaders of encouraging "voluntary apartheid" in Britain by shutting themselves away in closed societies. "We have to give some real thought to ensuring that we don't have a society that develops on parallel lines," he said.
Mr Davis backed the Commons leader Jack Straw, who ignited the controversy over the veil by saying that he asked Muslim women to remove it whenever they attended his constituency surgery.
Objections from faith schools and Catholic adoption agencies have delayed government plans to stop schools, companies and other agencies refusing services to gays and lesbians.
Alan Johnson, the Education Secretary, is urging the Cabinet not to water down new gay rights legislation but Ruth Kelly, a devout Catholic and the Communities Secretary, is said to be sympathetic to the protests.
European attitudes
* FRANCE
Headscarves and other religious symbols, including Jewish skullcaps and large Christian crosses, were banned in French state schools from September 2004. The law was aimed at maintaining France's tradition of separating the state from religion. It did not explicitly mention any symbols, but was considered by some as targeting Muslim schoolgirls.
* DENMARK
The headscarf can be worn in the public domain but is partially banned in private sector. Students and teachers can wear the hijab. During the summer of 1999, in a high-profile case, the two largest Danish chains of supermarkets stated they did not wish to employ Muslim women wearing headscarves. They claimed that headscarves were unhygienic and not compatible with their principles concerning uniforms. But companies have been fined for imposing prohibitions.
* TURKEY
Women are banned from wearing headscarves in state-controlled areas, such as universities and government offices, despite the majority of the population being Muslim.
The ban is based on the Turkish constitution's principles of secularism and equality and was upheld by the European Court of Human Rights after a Turkish woman took the state to court over the issue in 1998.
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