Cemex UK Properties admitted some of the plantation would be affected at the site that also skirts the location of the historic 1526 Battle of Linlithgow Bridge.
The Woodland Trust Scotland charity said it is angry that Cemex, whose UK HQ is in Surrey, is planning to build houses at the award-winning new woodland on the edge of the West Lothian town. The charity said six hectares of woodland dominated by birch, oak and ash were planted in 2012 close to the historic battle site as part of the restoration of a Cemex's former aggregates quarry at Kettlestoun Mains.
The restoration site was commended in the New Native Woodland category of Scotland's Finest Woods Awards in 2013, sponsored by the woodland charity.
Carol Evans, director of the Woodland Trust Scotland, said: "Ripping out these saplings after just two years would be disgraceful. The planting was commended in Scotland's Finest Woods Awards because the new woodland has been well planned and planted to a high standard, within an area that has been opened up for people to explore and enjoy.
"Less than a fifth of West Lothian's woodland is native, which makes creating new woods in the area really important.
"We're asking Cemex to reconsider their plans and stick to the original proposal to plant a woodland that benefits people and wildlife, and that creates an attractive green gateway to Linlithgow."
A spokesman for Cemex said yesterday the concerns were "overstated", adding: "There only seems to be a small area that is affected on the eastern boundary and the vast majority of the planting scheme would remain intact."
The firm has put forward a "proposal of application notice for planning permission in principle for residential development" which is the early stages of the planning process with West Lothian Council.
The application said a full consultation was planned with the community as well as politicians.
It said in the paper that a "consultation event presenting indicative plans for comment and attended by the projects' professional consultant team including representatives of the applicants was planned".
"Oral comments will be recorded at the exhibition, while questionnaires will also be available to record and provide a forum for written comment."
The firm was earlier criticised for plans to extend a quarry at New Lanark World Heritage Site which is being examined by the Scottish Government. The move came after South Lanarkshire Council approved a plan by Cemex to extend Hyndford Quarry into a zone surrounding the mill town.
Cemex UK Operations wants to stretch its sand and gravel quarry inside the buffer zone, which is part of the Clyde Valley Woodlands National Nature Reserve, a special area of conservation.
The the examination of the Hyndland Quarry proposal is ongoing.
A spokesman for Cemex said: "We were pleased that the original planning application was approved by South Lanarkshire Council.
"We hope and trust that the process that is currently underway will confirm that decision."