The company, formed by the Government to develop and promote the UK's high-speed rail network, says it has assessed 11 ancient woodlands which were due to be affected by rail preparations between London and Crewe this autumn.
Work on these will now be deferred to Autumn or Winter 2020 on five of these sites, and to early 2020 on the remaining six.
"We will also take measures to protect wildlife to ensure they are not affected when work begins in early 2020."
Is said prior work on the six sites "will involve some localised removal of selected tree branches for essential protected species mitigation works", adding: "We will not remove branches from any 'ancient' or 'veteran' trees within an ancient woodland so as not to affect the integrity of the ancient woodlands."
Other essential preparatory works will continue including low level vegetation clearance, fencing and preparation of site accesses, it said.
HS2 claims that of the 52,000 ancient woodland sites in England, 43 will be affected by HS2's route between London and Crewe, and over 80% of the total area of these 43 will remain intact and untouched.
Work on the multi-billion-pound infrastructure project has been paused while the Government-commissioned Oakervee review considers "whether and how to proceed" with it.
The Woodland Trust, which has campaigned against the project's incursions on ancient woodland, has welcomed the delay in clearing the sites, but says it is concerned about the ongoing work at some of them.
Its director of conservation and external affairs Abi Bunker said: "The richness of ancient woodland isn't just about trees. It's also the vegetation, the soils and the wildlife that makes ancient woodland a special irreplaceable habitat.
"Work that permanently affects these habitats like clearing vegetation and evicting bats and mammals must be stopped too while the review is completed."
The trust says contractors attempted to start work translocating soils from at South Cubbington Wood, Warwickshire on 30 September - "exploiting a loophole" in the pause to the programme.
It claimed the contractors employed at the site have never carried out ancient woodland translocation before.
"We have repeatedly told HS2 there is very little evidence to suggest translocation works," Woodland Trust ecologist Luci Ryan said.
"The Trust has repeatedly asked to see its methodology but to no avail."