Earlier this year, the Department for Communities and Local Government (DCLG) consulted on plans to exempt schemes of 10 homes or under from providing affordable housing, obtained through section 106 planning gain agreements.
But the proposals put new affordable housing in national parks at "serious risk", the 10 park authorities' chairmen say in a joint letter.
In national parks, most development sites are typically small, involving infill opportunities or conversions to provide cheaper housing, they point out.
The introduction of any threshold, according to the letter, "will considerably reduce the ability of national park authorities in our efforts to respond to the high levels of local housing need in many of our communities".
It adds: "Indeed, removal of the ability to use section 106 agreements on small scale schemes will mean that the community in at least one national park will not be able to meet their aspiration for local needs housing set out in their adopted neighbourhood plan.
"We are clear that only an exemption for national parks from this particular proposal will avoid the serious unintended consequences for affordable housing.
"The need for new affordable housing is just too great, that any change that makes it harder rather than easier to deliver new affordable housing in national parks will be felt acutely by our rural communities."
The move was first announced in last year's Autumn Statement, when the government said that it would reduce costs for small builders and boost housebuilding.
The government consultation, which closed in May, proposed excluding 'rural exception sites' from the provisions, but the national park authorities argue that this would only be a partial safeguard because such sites are normally greenfield sites on the edges of villages.
The chair of umbrella body National Parks England and the North York Moors National Park Authority, Jim Bailey said: "These changes go to the heart of how we can respond to the need for affordable housing in our rural communities.
"The national park authorities are committed to supporting living working communities This proposal simply won’t help that in rural areas and we hope the government will listen and exempt national parks from the change."
A DCLG spokesman said: "People working hard and wanting to build their own home or developers looking to build a small number of properties should be able to do so without paying out excessive charges.
"There are currently too many levies and charges on housing and why we want to cut them to help support hard working families, give small builders a boost and build more homes.
"These reforms will help increase both house building and housing supply, and lower the construction cost of new build housing and home improvements.
"We’ve made very clear that the threshold would not apply to rural exception sites. The consultation has now closed and we are considering responses including those from the National Parks."
He added that the government is considering the 300 consultation responses before publishing its own response later this year.