One of Scotland’s most controversial road developments could be stopped in its tracks by a few colonies of roosting bats, wasting £51 million of taxpayers’ money, say campaigners.

Soprano, pipistrelle and brown long-eared bats have been discovered in the International School of Aberdeen, which is set to be demolished to make way for the new Aberdeen bypass.

The bats are protected under European law, making it illegal to destroy their roosts unless suitable alternatives are provided for them nearby. According to experts that means it will be “impossible” to knock down the school.

A decision by the Scottish Government on whether or not to give the Aberdeen Western Peripheral Route the green light is overdue. Ministers have been considering a secret report from last year’s public inquiry since July.

But the Government has already promised to pay £51m to help the international school relocate. This will turn out to be a colossal waste of money because of the bats, according to the local group Road Sense, which is opposed to the Aberdeen bypass.

“As the law stands there is no possibility that the existing school could be demolished,” said Nigel Astell, an environmental consultant who lives locally.

“European law forbids the demolition of buildings containing bat roosts, especially if there are alternatives available. Transport Scotland deliberately chose a route for the road that went straight through the existing school, even though other options were examined that could have avoided this.”

Under the law, it is a criminal offence to intentionally or recklessly disturb a bat in its roost, deliberately disturb a group of bats or damage or destroy a bat-roosting place.

Road Sense has lodged a formal complaint with the European Commission, alleging that the Scottish Government would be in breach of the law if the school is demolished. Sheona Warnock from Road Sense pointed out that the Government had also spent millions promoting the new road, despite the fact that it had not yet been approved. “What a disaster!” she said.

“It’s a black hole for money that could be better spent on improving public transport or public services. The project has been incredibly badly conceived, devised and managed from the start, and it is now looking very likely that it will not be able to go ahead.”

The Government’s conservation agency, Scottish Natural Heritage (SNH), confirmed that protected species of bats had been found at the school.

“A licence to destroy the bat roosts through the demolition of the building will be required from the Scottish Government,” said an SNH spokesman.

“As part of the licence application a mitigation plan will be required to be produced which includes the provision of an alternative purpose-built roost building close to the site of the original buildings.”

Local campaigners were backed by the Green MSP Patrick Harvie, who condemned plans for the proposed bypass as “a very expensive series of cock-ups”.

He questioned whether it was right to spend public money on a project that had not yet been approved and called on ministers to abandon it.

“The road has been a bad idea from its inception and has always been designed to gain votes rather than solve the traffic and transport problems of the north east. If this administration or its predecessors were serious about these problems, the money would have been spent getting Aberdeen Crossrail up and running and supporting better bus services.”

A spokesman for the Scottish Government said: “The issue of bats and other protected species were considered as part of the public local inquiry.

“Ministers are considering the report and recommendations from the inquiry, and will respond in due course.”