The working rules for Whitehall and the Scottish Government to confront a renewed outbreak of foot-and-mouth disease need to be updated urgently, according to an independent report.

The official investigation into the impact on Scottish farming of last year's outbreak of the disease in Surrey by former chief veterinary officer Jim Scudamore, published yesterday, concluded there may be a need for all "hobby farmers", who keep farm animals but not for commercial reasons, to officially register.

It also called for rules on hauliers' working hours to be relaxed when there is a farming crisis and sheep and cattle need to be moved quickly for welfare reasons.

One of the key recommendations taken up by Scottish Rural Affairs Secretary Richard Lochhead is that the response to an outbreak should be "regionalised", meaning the clampdown on animal movements and exports should be relaxed much sooner in areas distant from the affected area.

The report found that the concordats, the rules of engagement between Scotland and Whitehall which were drawn up in 1999, are no longer fit for purpose.

Mr Scudamore, who has worked in the Scottish administration and later as chief vet in Whitehall, said they should be renegotiated each time there is a change of government.

While Scottish policy on handling a farm disease outbreak lies with the Holyrood administration, the finances are held by the Department of the Environment, Food and Rural Affairs (Defra) in London.

That led to a spat between the two governments last year, when Defra signalled that it would help out farmers who had lost out by being unable to move sheep off hillsides at a crucial time of year. Mr Lochhead accused them of going back on that and leaving it to his department to foot the bill.

The report recommends that finance for animal welfare payments should be held by the Scottish Government. But a major outbreak requiring mass slaughter should still be for the UK Treasury to compensate through its contingency reserve.

Last year's outbreak in Surrey forced an end to all farm animal movements in the UK, including the Scottish islands.

The farming and linked industries in Scotland reckoned it cost them around £100m. Compensation payments from the Scottish Government ran to £25m.

The report found there had been "misunderstandings" about the announcement of relaxed rules on animal movements, as a result of confused communications between Edinburgh and London.

Differences between them led to "friction".

"There has been a perception in England that a number of the actions taken by the Scottish Government were purely for political reasons and not related to best scientific and veterinary advice," Professor Scudamore wrote.

"From the evidence available, this does not appear to be the case. The Scottish Government took appropriate action based on the best veterinary and scientific advice available."