The present system, under which some landowners receive large payments merely to avoid carrying out damaging activities, is to be scrapped, and replaced by one in which payments are only made for positive conservation work.
The proposals were unveiled in response to concern about the health of Britain's 50-year-old network of Sites of Special Scientific Interest (SSSIs), the 6,400 areas of woodland, meadow, mountain, heathland, bog, and river valley that have been designated as important for their flora, fauna or geological features.
Most are privately owned and the Government has hitherto relied on a voluntary approach for their management, but they are being degraded by inappropriate farming practices, housing and road development or simple neglect, and plants, insects, birds and animals are disappearing.
Earlier this year the Royal Society for the Protection of Birds said the network was in crisis, that one in five sites had been damaged in the past five years and that nearly half were suffering from neglect or mismanagement.
Yesterday Mr Meacher moved to tackle the problem with proposals for better protection for the 5,000 sites in England and Wales (similar proposals for Scotland will be announced next week).
"They are our finest and most important conservation and geological areas, and our most significant and often most fragile habitats, and they are home to some of our most threatened species," Mr Meacher said. "But their framework of protection is not adequate."
The Government is proposing the wildlife agencies that oversee the SSSI system (English Nature and The Countryside Council for Wales) should be able to refuse permission for any operation which damages a site's conservation interest, such as the ploughing of a chalk grassland.
At present they can only delay it for four months while they try to seek a management agreement with the landowner, unless the Secretary of State for the Environment intervenes directly, something that happens rarely. In future, if damaging operations go ahead despite the prohibition, the landowner could be prosecuted and tougher penalties imposed, with persistent or repeated offenders subject to an unlimited fine, in contrast to the present statutory maximum of pounds 2,500. Magistrates would also be given power to require restoration of the damaged land, which might be even more costly.
The much-criticised scheme under which landowners could receive large and secret payments for "profits forgone " - for not doing something potentially damaging - is to be scrapped and replaced with payments for positive conservation management.
Mr Meacher indicated that the details of such future agreements were likely to be made public. The Government recognised that most landowners and farmers were responsible in the way they handled SSSIs, but a minority were not.
The Government will investigate the possibility of refusing to pay EU grants which result in sites being damaged, and thinks there should be special powers to stop damage to sites from "third parties", such as motorcycle scramblers. Planning guidance about developments involving sites is also to be toughened.
The proposals are out for consultation and there is no time in the coming parliamentary session to bring in the legislation they will need, although Mr Meacher is keen for it to go ahead as quickly as possible.
Environmental groups that welcomed the proposals said converting them into law was a key test of the Government's commitment to the environment. "Michael Meacher and John Prescott have signalled their support for these changes but only Mr Blair can give them the ability to make them," said Tony Juniper, Friends of the Earth campaigns director. "If this is not in the Queen's Speech in 1999 this government will not have the right to call itself green, as it did in the election to get people's votes."