The attack happened on the eve of the summer solstice, when Avebury becomes a shrine for hundreds of Druids from all over the UK.

Historian Professor Ronald Hutton said the attack was "appalling" and was akin to desecrating a church on Good Friday.

The stones were painted red, green and white by a gang who struck in the early hours of Friday morning.

Giant tomatoes

An anonymous caller to the BBC in Manchester said the attack was undertaken as a protest against GM foods. He said the stones were painted red to represent giant "freak" tomatoes.

Wiltshire police spokeswoman Elizabeth Marginson said the force received a call from a member of the public who noticed the vandalism at 0440 BST.

First farm-scale GM crop trial carried out in Wiltshire

She said: "There were reports of criminal damage to two stones in The Avenue at Avebury."

Ms Marginson said the National Trust, who were responsible for the site, and the police were working together to get to the bottom of the case.

A National Trust spokeswoman said the two stones in question had been "wrapped" to prevent further damage.

GM crop trial aborted

It is thought Avebury may have been targeted because of the proximity of the site to the first farm-scale trial of GM crops.

Fear GM crops could damage wildlife

Last week, the farmer who volunteered to use his land at Hannington, Wilts, as a test site destroyed the crop on the orders of the farm's trustees.

Captain Fred Barker said he had been keen to examine the possibilities of GM crops but his trustees were opposed to the government-run trials and were unhappy that other crops on the farm were to lose their organic status because of the trial.

The 26-acre crop of GM rapeseed was planted at Easter. The company which developed the GM crop seeds, AgrEvo, said it was "deeply disappointed" at the trial being aborted.

Prof Hutton, a professor of history at Bristol University, said Avebury was a site of huge historical and scientific interest.

'Cathedral for pagans'

He told BBC News Online: "It was once said that it surpasses Stonehenge like a cathedral surpasses a parish church."

Prof Hutton said the protesters had no doubt targeted the site because it would be high profile with the coming of the solstice. But he said: "They have damaged part of our history while demonstrating about our future, which is crazy."

Two years ago strange symbols were painted on the stones by vandals.

Prof Hutton said removing the paint would be costly and would damage lichens on the stones which were of great biological interest.

He said Avebury, which is situated in the middle of a village, was a large site which was more difficult to fence off than Stonehenge.

"Fencing off the site would be impractical and tragic," he said. Avebury stone circle is more than 4,000 years old and was built between 2,600 and 2100 BC.