The size of the bill could force some dioceses to sell struggling schools or transfer them out of Church control so the Government will pick up the tab.
The figure is contained in a report published this week by the Las Casas Institute at Blackfriars Hall, Oxford, which called the move 'a smash-and-grab raid on the Catholic community'.
Diocesan officials across England and Wales are deeply worried about the cost and are trying urgently to work out a national strategy to deal with it.
The report, entitled Ed Balls, Michael Gove and the Challenge to Faith Schools, said: 'While professing public support for faith education in public... deep below the surface of public conversation and beyond the debates of Westminster, the Secretary of State has been introducing detailed rules that represent a smash-and-grab raid on the Catholic community and the wide range of stakeholders who benefit from its schools and their community service.'
The £100 million represents 10 per cent of the total cost of renewing Catholic primary school buildings under Government plans over the next 12 years. The plans, known as the Primary Capital Programme (PCP), were introduced after it was reported that the run-down state of buildings was harming children's education.
The previous school rebuilding programme, called Building Schools for the Future, was funded entirely by the Government.
In contrast the PCP requires a total of £350 million from the whole faith school sector. Each diocese is expected to negotiate the bill separately with all the local authorities in its area. Sympathetic local authorities may offer to pay some of the money if - as is likely in some cases - the diocese cannot afford it.
However, it is thought that the Conservative Party would pay in full for faith school rebuilding programmes - which would mean that the cost to the Catholic community would be nothing.
Stephen Morgan, chairman of the conference of diocesan financial secretaries and financial secretary of Portsmouth diocese, said: 'It's a really big problem, and a problem we don't have a way of solving at the moment.
'The Catholic community is growing and the new arrivals are not wealthy. It's all very well to ask Catholics in the leafy suburbs to pay extra money but it's more difficult if they are from Ghana or eastern Europe and living in the East End of London.'
Gerald Curran, financial secretary of Brentwood diocese, agreed that it would be very difficult for dioceses to raise the funds. He said: 'Basically the dioceses would not have that sort of money - it's a huge amount of money. Those primary schools that needed work would be immediately dealt with but others would have to be put on the long finger.'
Noel Loughrey, financial secretary of Salford diocese, said: 'It's clearly going to be difficult to raise the 10 per cent because of the sheer size of the sums involved.'
Martin Lockery, schools commissioner at Salford diocese, said it would be 'difficult, probably impossible' to raise the money - but that good relationships with local authorities meant the diocese would not have to pay the full 10 per cent.
He said one £6 million project to merge two schools into one - as part of the PCP - was funded entirely by Manchester City Council.
'We have ongoing conversations about what we can afford. The [Manchester] authority was well aware that suddenly having £600,000 thrown our way would be a non-starter. It was an acceptance of the reality of the situation,' Mr Lockery said.
No help from the CES
One financial secretary said dioceses had received no help at all from the Catholic Education Service. 'It was not even on the CES's radar - or if it was, they didn't let us know about it,' he said. The Catholic Education Service was not available for comment.
According to the Las Casas Institute report the £100 million bill is just one of a series of 'raids' by the Government on Catholic schools.
The report discloses that the Government has withdrawn its insurance cover for school buildings, transferring it to local authorities which are then not obliged to provide it.
In Hull, for instance, the local authority has demanded that Catholic schools pay for their own insurance. If this move were repeated across the country, the report says, the cost to the Catholic community would be £30 million a year.
The report also points out that under current Government regulations the Church cannot keep the proceeds from a sale of a school unless they are reinvested in another school in the same area. This means that if the Church tries to adapt to changing Catholic demography - to respond to an increasing need elsewhere in the diocese - it could lose tens of millions of pounds of assets.
Some claim the report is likely to reinforce a sense among Catholics that the Labour Government is hostile to Catholic education.
Last year Schools Secretary Ed Balls accused faith schools of breaking the admissions code in an 'unacceptable' way. Months later, a report by the schools' chief adjudicator said the vast majority of admissions arrangements at Catholic schools were 'fair, transparent and fully compliant'.
In 2006 the Government sought to impose a 25 per cent quota of non-Catholics on Catholic schools but was forced into a U-turn after pressure from the Church.
A spokesman for the Department for Children, Schools and Families said: 'The £1.9 billion Primary Capital Programme will rebuild or improve at least half of all primary schools in England, so that they reach 21st-century standards and help provide wider services for children and families in their communities.
'Since an Act of Parliament was introduced in 1944, it has been a requirement that voluntary aided schools contribute to the cost of any building work that takes place. Local authorities can, of course, assist voluntary aided schools with this contribution if they are able.' [Catholic Herald]