His move came as the Prime Minister continued to resist pressure to put off the elections due in early May.
The deepening crisis has prompted further calls from farmers' leaders and local politicians to postpone the English council elections due on 3 May.
Prince Charles said six charities would benefit from his donation, which was aimed at easing the plight of farmers under severe strain from the "dreaded outbreak".
He said: "Many farmers throughout the UK are facing desperate hardship at the moment.
"Even those whose farms have so far escaped the disease have rightly had severest restrictions put upon the movement of their stock."
A St James's Palace spokeswoman said the money was from income raised by Prince Charles's charitable activities.
The Prince said: "I want to do everything I can to help these farmers and their families to keep their heads above water.
Suicide risk
The Prince, who had been criticised for demanding the rent due on farms in his Duke of Cornwall estate, added: "This dreadful outbreak is also imposing severe stress and anxiety on many individuals and farmers - there can be no doubt that the risk of suicides among rural communities is heightened at the moment.
"Having someone to talk to who understands the problems can make all the difference."
On BBC2's Newsnight programme Environment minister Michael Meacher welcomed the contribution.
May 3 is the day widely tipped as Tony Blair's choice for the general election.
Nigel Henson, Director of Communications for the Countryside Alliance said he hoped the Prime Minister would make allowances for the fact that rural Britain is facing its biggest crisis for 30 years.
He said the timing of any election should be "in the interest of the electorate, not in the interest of the government".
But Mr Meacher said there was no intention to change the date as yet saying the issue depended on "the future course of the outbreak".
National Farmers' Union president Ben Gill said it would be "totally unacceptable" to have a ballot on 3 May while country people were effectively disenfranchised.
"You can't ask farmers to think about an election when they're up to their eyes in uncertainty and fear," warned Peter Chalke, leader of Wiltshire County Council in one of the worst-hit areas.
In the Commons this afternoon, Mr Blair announced a programme of "intensified slaughter" of tens of thousands of sheep to try to control the spread of foot-and-mouth.
"We are looking at how we step up the slaughter in those areas most directly affected," he told parliament.
"It is entirely right that we look to see how we take more urgent measures in those areas."
He said it might be a "sensible precaution" to cull animals which had come into contact with the disease even if they showed no symptoms themselves.
The government pledged on Wednesday to do all it could to help a "devastated" tourism industry from losing a potential £250m a week as it approached the main summer season.
Culture Secretary Chris Smith said bookings from within the UK and from overseas were being cancelled just at the time of year when trade usually picked up.
"Rural Britain is not closed as some would have us believe," he told MPs in a Commons statement.
"We have to make sure that as soon as the outbreak is over the message of 'come back to the countryside' must be made loud and clear."
Brushing aside questions of compensation, Mr Smith said the best thing to do at the moment was to encourage people to go to the countryside for safe activities.
The disease has now spread to mainland Europe which has prompted Australia, New Zealand, the United States, Canada, and dozens of other countries to impose a temporary ban on the import of all livestock and meat products from the European Union.
France had hoped to escape the outbreak with stringent measures, but confirmed its first case on Tuesday.