The firm has suspended work at the majority of sites until further notice, but is planning to continue at a five sites across the region which are considered crucial to the delivery of the controversial scheme.
The decision has prompted a furious reaction from the Woodland Trust, which says the areas face "imminent death" at a time when they should be "bursting into life".
HS2 plans to use "translocation" to move soil from the sites in question to new plots nearby, but critics say this should only be considered in late autumn, and then only as a last resort.
One of the sites set for work is Fulfen Wood near Lichfield, which is set to be subjected to "a wanton act of desecration" according to Conservative MP Michael Fabricant.
He said the work would "destroy" at least an acre of ancient woodland, which contains both common and soprano pipistrelles bats and occasional Myotis species.
"Bat roosts within this wood will be lost to the scheme," the Lichfield MP added. "I agree with the Woodland Trust who say that HS2’s attempts to move the soil from five ancient woodlands during April is a futile act.
"The move goes against both conservation principles and guidance from Natural England. Ancient Woodland is at least 400 years old and which has remained undisturbed during that period."
The other affected sites – Broadwells Wood, Birches Wood, Crackley Wood, and Ashow Road – are all in Warwickshire. The work is expected to take around eight weeks.
Woodland Trust ecologist Luci Ryan said: "Instead of bursting into life, these irreplaceable ancient woodlands now face imminent death.
"Attempting to move ancient woodland soils from one site to another is flawed. Attempting it in April doubly so.
"Add into the mix that the contractor doing it has never translocated ancient woodland nor visited a translocated site and it’s a recipe for disaster. It’s like getting a bike mechanic to service a Boeing.
"HS2 Ltd has admitted it is acting against industry standards by doing the work now, when ancient woodland is bursting into life.
"We are shocked at their approach. Protection of the environment continues to play second fiddle to costs and timetables."
Concerns have been raised over HS2 Ltd's decision to continue work during the Covid-19 lockdown, with Tory MP Rob Butler telling the Commons he was concerned that HS2 contractors were not following safety advice.
A HS2 spokesman said: "To ensure the health, safety and wellbeing of our workforce and the communities in which we are working, only construction sites that can maintain government guidelines and are critical to the delivery of HS2 will remain operational.
"As a result, the majority of our sites have paused, or are pausing, construction works.
"Those sites still working are doing so because they are confident they are operating within PHE guidelines and will remain under constant review."