The local bishop, who had previously had beehives placed on his episcopal church, came up with the idea.
He left the 60 or so hams a year to mature in one of the two bell towers for up to a year.
They were then sold under the name "Florus Solatium" in delicatessens and French gourmet kitchens, bringing the diocese some additional income for the preservation of the cathedral.
However, the ham is a problem for the monument protection authorities: dripping fat is attacking the cathedral and the ham legs are blocking access to the tower, they criticise.
The French Minister of Culture has now intervened in the dispute.
In a press release published on Wednesday, it states: "The Minister of Culture wants a new trial to be carried out, at the end of which a transparent and comparative balance sheet will be drawn up, taking into account all fire safety conditions in particular."
According to the press release, there should be no end to the curing of hams in the cathedral.
The minister has "an open ear for the local MPs, the diocese and the craftsmen and caterers in this matter".
She is now asking for innovative solutions that will enable "the national territory, its cultural heritage and its gastronomy to be showcased".
Saint-Flour Cathedral, formerly a priory church of Cluny Abbey, is the highest episcopal church in Europe.