The aim of the swoops is to ensure that crofters are not claiming grants for more sheep than they own. But the system is hated because - under EU regulation 3887/92 - more than half the checks have to be conducted between February and May.
This is not only the time of year when the weather is at its fiercest but also when sheep are about to lamb. Crofters are disturbed at the way such regulations clash with their easy-going traditions of co-operation and working by rule of thumb.
Donald McLennan, a crofter with 180 sheep in Harris, is dreading the EU inquisition. "This year it's been pouring all the time, which means that you cannot get on the hills," he said. "The sheep are in lamb, and a spot check could mean they die of cold if they're forced out of their shelters. It's impossible to have a full gather at short notice."
Crofting is the antithesis of modern farming, with sheep left to wander the moors, gathered only for dipping and shearing. It is also a part- time job, providing as little as five per cent of crofters' income.
Crofting representatives and Scottish Office officials have been to Brussels to protest. Scottish Crofters Union advisor Fiona Mandeville said: "These regulations were drawn up by bureaucrats in offices hundreds of miles away. They have no understanding of practices in these remote areas." She says the regulation was designed for warmer climes where farmers can count their sheep by looking out of the window.
The Scottish clampdown is the latest sign that Brussels is determined to stamp out fraud in the claiming of its grants and subsidies, following reports that millions of pounds are being lost.
Tales such as the 1,500 cattle being registered at a penthouse apartment address overlooking Piazza Navona, in central Rome, have intensified pressure on the European Commission - as did a case in 1993 when 63 consignments of tobacco were exported to Romania from Italy, attracting subsidies of pounds 11.75m. Inspectors found the containers contained paper, plastic and mouldy tobacco. In total, since 1994 there have been 4,168 cases of fraud detected in the EU, amounting to a bill of pounds 800m for the taxpayer.
In addition to spot checks, Brussels is demanding that agricultural census survey forms are filled in for grant applications, showing numbers, breeds and ages of animals and accurate maps of holdings.
Smaller crofters have decided the work is not worth the trouble and eight per cent have given up applying for grants. The Crofters' Commission fears that some could give up crofting altogether as a result.