On 6 December, HS2’s contractors Fusion moved into areas of the nature reserve - a 20-hectare open-water habitat in Buckinghamshire - and begun clearance works without giving notice.
The works came to the trust’s attention due to alerts from members of the public.
The trust said that HS2 had entered around a third of the reserve and started chopping down trees which housed bats.
HS2 originally claimed the works were “essential” and that they had “full permission of the landowner” to engage in the work.
However, in a letter seen by ENDS, David Bennett, delivery director for HS2 said: “We are sincerely sorry for this work having taken place on land, for which we did not have permission.”
A spokesperson for HS2 said the work was carried out “based on incorrect information as to who owned the land, and whether consultation had been taken place in advance”.
They confirmed that no further work would take place until a full investigation has been carried out.
“I hope we can rebuild a positive relationship between BBOWT and HS2 as we move forward,” added Bennett.
BBOWT chief executive Estelle Bailey said: “We want HS2 to work to a higher ecological standard than they’ve shown so far at Calvert Jubilee nature reserve.
“It is absolutely nonsensical for irreversible works of destruction to take place while the whole of the HS2 project is being reviewed.
“We expect that HS2 entering our nature reserve and destroying habitat was a one-off incident. We are concerned about the threat of extinction of a number of species. as a result of their actions.”