In particular, the Government's policy of blanket countryside closures had a devastating effect on the rural economy, according to the National Trust.
The Government's response to the crisis was ill-thought out and ineffective, failing to think beyond the interests of agriculture, argued the charity in a formal submission to the inquiry.
Peter Nixon, the National Trust's director of conservation, said: "The most important lesson of foot and mouth is the need for a wider understanding of how disease control affects rural prosperity. The failure to plan beyond the interests of agriculture made a bad situation even worse."
Roger Clarke, chief executive of the Youth Hostel Association (YHA), said the Government was partly to blame for the fact that 10 YHA hostels will be sold later this year to help plug a £4 million hole in its finances sustained as a result of the countryside closures.
"The Government made a serious mistake in closing the countryside. It should have been more selective in the closures," he said. The Government gave the public the impression that anywhere outside major towns and cities was a no-go area, rather than telling them to keep away from livestock in infected areas, which would have saved us a lot of money."
According to YHA, which passed comments on to the inquiry, the Government also took too long to re-open closed areas.
The YHA is not the only charity that suffered financially. The National Trust estimated that it lost ?xA3;4.5 million because of extra costs and the decline in visitor numbers. The British Trust for Conservation Volunteers (BTCV) said it lost at least ?xA3;500,000, which led to 25 staff being laid off.
BTCV chief executive Tom Flood told ThirdSector that the Government had not even discussed the possibility of compensation with groups in the sector.
"We would like to see more recognition of the problems experienced by organisation in rural areas," he said.
"Conservation charities are a long way down the queue when it comes to compensation. There isn't a mechanism I can identify where we'd qualify for any money."
see YHA story, p4.