Trees were felled and the potential habitats of rare bats and butterflies were destroyed on a nature reserve without permission to make way for HS2, the high-speed rail scheme has admitted.

Contractors sealed off public footpaths and removed trees inside Calvert Jubilee nature reserve, in Buckinghamshire, without notifying the landowner, the Berkshire, Buckinghamshire and Oxfordshire Wildlife Trust (BBOWT). Work which eradicated habitat where bats could roost was carried out in December, despite the government having ordered that “irreversible” destruction of ancient woodland should be halted unless deemed absolutely necessary while HS2 is under review.

When the trust raised the alarm after volunteers working at the nature reserve spotted the work being done, an HS2 spokesperson initially insisted it had acted with “the full permission of the landowner”. But in a letter to the wildlife trust seen by the Guardian, HS2 subsequently admitted it did not have permission to undertake the work.

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It claimed it had mistakenly believed the site belonged to another landowner from whom it had permission, despite contractors entering the site past signs clearly identifying it as a BBOWT nature reserve.

Mark Vallance, reserves manager for BBOWT, said he was “livid”, and it was alarming that wildlife habitat could be destroyed by accident.

“It terrifies me that this sort of thing can happen so easily,” he said. “We’ve talked to HS2 numerous times about the impact on our nature reserves.

“If HS2 doesn’t go ahead – and we accept that’s a slim possibility – then there’s been a loss of really good bat habitat here.”

Dozens of limbs from old ash and sallow were removed and several whole trees chopped down. Vallance said the destruction appeared to have deliberately targeted the best bat habitats. The presence of live bats – which are protected by law – has the potential to stop HS2 construction work, set to begin later this year.

Following widespread local protests against the destruction of ancient woodland while the high-speed line is under review, the transport secretary, Grant Shapps, ordered HS2 in September to “consider what works affecting ancient woodland clearances can be delayed for the duration of the review”.

But “enabling works” to remove ancient hedgerows and trees before the main contracting works are continuing apace, with miles of hedges grubbed up in recent weeks close to the proposed line through Buckinghamshire, Northamptonshire and Warwickshire.

A leaked copy of the review into HS2’s spiralling costs by Douglas Oakervee revealed he is set to endorse the project but his deputy, Lord Berkeley, this week issued a “minority report” castigating the project for “seriously misleading” parliament, with the estimated final cost rising to £107bn.

Boris Johnson admitted costs were likely to rise above £100bn during the election campaign.

Facebook Twitter Pinterest Activists demonstrating against the HS2 railway line in Denham, Buckinghamshire. Photograph: Stephen Bell/Alamy Stock Photo

Of the environmental damage, Lord Berkeley – a rail expert who has worked for Eurotunnel, the Rail Freight Group and as a transport minister – said: “Compared to improving existing lines, HS2 is not good for the environment, and HS2 Ltd has exacerbated the situation by its appalling treatment of stakeholders, residents, businesses and councils in the areas over which it plans to construct the lines.”

At Calvert Jubilee nature reserve, the high-speed line requires the removal of the eastern edge of the reserve, including orchid-rich grassland and scrub which until recently contained Buckinghamshire’s last remaining populations of nightingales and turtle doves, as well as all five species of hairstreak butterfly.

In a letter to BBOWT, David Bennett, the delivery director of HS2, apologised for undertaking work without permission and said it had incorporated feedback from the charity on the 75,000 trees it will plant this winter close to the nature reserve as compensation for the destruction.

Bennett said: “Over time these trees will connect areas of existing woodland … and form new bat flight lines away from the HS2 route.”

According to BBOWT, HS2 has repeatedly refused to provide it with precise information about how much of the nature reserve will be removed. Other landowners along the line have reported a similar lack of clarity.

“Every metre counts,” said Vallance. “Even if the land taken was reduced by a couple of metres, it saves a chunk of nature reserve because the track goes through so much of the reserve. Once it’s gone, it’s gone. You can recreate habitat but it takes an awfully long time.”

Like other landowners, BBOWT has not yet been paid compensation for land already taken by HS2. Another landowner, who asked not to be named, said compensation was being withheld to minimise local dissent. “Some landowners feel bullied by HS2,” they said.

Another landowner close to Calvert Jubilee, Christopher Prideaux, whose farm is bisected by the line, described being surrounded by “all manner of chaos” with expensive and ill-planned “enabling works” including the construction of “newt ponds without any newts” on productive farmland.

“This a national crisis,” he said. “I don’t think Westminster will care about the environment. Westminster will care about billions of expenditure.

“HS2 are hoping to get so far down the track that it is too difficult to cancel. This is not true. In financial terms, the first loss is the cheapest loss. What has been spent so far is a fraction of the overall sum. No government has got any right to be blundering ahead with this without a national transport policy.”

In his independent report, Lord Berkeley said HS2 was an “expensive” and “wrong” solution to improving the rail network and recommended spending half HS2’s budget on upgrading existing commuter lines, particularly in northern England and the Midlands.