Officials have complained that the "open-ended" budget for the four-day visit is spiralling out of control, as experts reassess critical requirements, mainly security at the large-scale public events to be attended by the Pontiff.
The emerging problems with a commitment that the coalition inherited leaves ministers facing the prospect of having to plough millions more into a one-off event while being forced to make savage cuts across public services.
The Catholic Church in the UK was forced to rethink key elements of the visit, such as policing costs and security considerations last month.
It is believed that the church, which originally expected to pay some £7m towards the visit, has so far managed to raise less than £6m.
Senior Conservative peer Lord Patten was subsequently put in charge of co-ordinating the Government's involvement.
But it has emerged that there is a growing "black hole" developing in the cost of the operation.
The bill, which has already risen from an original estimate of £8m to at least £12m, is now feared to be heading way beyond £20m.
The costs are divided into two categories: policing and non-policing. It has been established that the state will pick up the bill for policing, guaranteeing the Pope's security and maintaining safety at some 14 engagements, including three open-air events.
The non-policing costs, including accommodation and travel for the papal delegation, will be split between the church and the Government.
Foreign Office minister Henry Bellingham told MPs last month: "Discussions are under way to finalise these costs and to agree the appropriate levels of contribution from the Government and the Catholic Bishops' Conferences of England and Wales, and of Scotland."
However, The Independent on Sunday understands that the church has so far managed to raise only £4m from the laity and £1.1m from a Pentecost Sunday parish appeal.
It is believed that the greatest concerns are over the cost of securing and controlling the three open-air events in Glasgow, Birmingham and London.
A number of groups have vowed to mount protests against the visit, citing allegations of child abuse by Catholic clergy and the record of the church on contraception and equal rights for homosexuals.
Officials had their fingers burned by a dramatic "cost miscalculation" last year, when the £7m estimate for London's G20 summit proved wildly optimistic. The final cost for the one-day, one-venue event was closer to £20m.
"It seems strange that the likely shortfall has only cropped up now," a senior source close to the planning operation said last night.
"But there are so many important things that just weren't considered closely enough. There is a worry that the sheer size of a modern security operation has not been taken into account, and the original costings were undershot."
The Pope is due to celebrate Mass before 100,000 people in Bellahouston Park, Glasgow, on the first day of his visit; hold a prayer vigil in Hyde Park; and mark the beatification of Cardinal Newman, in Birmingham's Cofton Park, on his last day in the UK.
Pope John Paul II made a pastoral visit to the UK in 1982, but Pope Benedict's trip will combine both pastoral and state business. He will be received by the Queen in the Palace of Holyroodhouse in Edinburgh.
A delegation from the Vatican visited the UK last month to discuss the visit with government officials and the Catholic Church.
Lord Patten, who is a Catholic, has conceded that the taxpayer's contribution will rise, although he insisted that the Government had "driven down the costs of some elements of the visit".
He also said he believed the church would raise more money for the visit.
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