Ministers have let voluntary-aided schools off their traditional 10 per cent capital contribution for the secondary Building Schools for the Future scheme.
But voluntary-aided primaries will have to pay their way in the new pound;7 billion programme announced this month.
Martin Bradshaw from the Catholic Education Service said it had only found out last week and was still working out whether its schools could afford the work.
"It is obviously going to cause a strain and it may be that further discussions with the Government are necessary," he said.
Rebuilding or refurbishing half of all of the Catholic Church's 1,723 voluntary-aided primaries in England by 2022, in line with the rest of the primary sector, would cost around pound;68 million.
The Department for Education and Skills has said: "Our view is that the proposed primary programme is different in scale and funding approach to Building Schools for the Future and that it is therefore reasonable to expect voluntary-aided schools to contribute as normal."
The Church of England, which has around 2,000 voluntary-aided primaries, would be left with a bill for around pound;79m.
Canon John Hall, Church of England chief education officer, said it would be beyond individual dioceses to find all the money.
Schools would also have to rely on fundraising from a variety of sources, but he said this could be positive.
"Although it sometimes looks like a very difficult target, fundraising can bring communities together," he said.