The destruction of a rare colony of tiny ants in the Cairngorms has prompted accusations that government agencies are failing in their statutory duties to protect wildlife.

The most northerly known nest of shining guest ants was smothered by clay when a forestry track was widened at Baddengorm near Carrbridge. Investigations into the incident have led to a land manager being reprimanded and delays to maintenance work on other forestry roads.

But it has also triggered claims the Forestry Commission and the Cairngorms National Park Authority are breaking the law by permitting such damage to occur – and that it could happen again unless remedial action is taken.

Shining guest ants are an elusive, unusual and ill-understood species. They are just three millimetres long, and live as "guests" in the distinctive mound-shaped nests of hairy wood ants on the floors of pine forests.

The larger wood ants seem to tolerate their presence, enabling them to survive by borrowing food.

The damage on a private estate at Baddengorm was discovered in February by Dr Murdo Macdonald, a biologist who has studied ants in the Highlands for the past 25 years. He reported it to the authorities, but is now concerned that lessons have not been learnt.

"Wood ants – vitally important keystone species in forests – are under threat from unsympathetic management by Forestry Commission and the Cairngorms National Park, who have a duty to protect them against undue disturbance," he told the Sunday Herald.

"More ants – and along with them the diversity of wildlife for which the Cairngorms are internationally renowned – are threatened by future forestry developments, unless the commission and the park work together to ensure that impacts are minimised."

Other countries were better at recognising the importance of ants as a way of naturally controlling pests, Dr Macdonald argued, "but here they seem to be regarded as unimportant by foresters."

He complained that proposed road maintenance in the commission's Inshriach forest on the west side of the Cairngorms could do further damage to ant nests.

Gus Jones, from the Badenoch and Strathspey Conservation Group, accused the national park of failing to protect important species. "New protocols, which must be followed on the ground, are urgently needed to tackle the problem of damaging forestry operations," he said.

The Forestry Commission described what happened at Baddengorm as "bad practice" and has formally admonished the land manger concerned. The work was carried out without the commission being consulted, it said.

At Inshriach, the commission said it called in Dr Macdonald after staff noticed ant hills. "We have since postponed work there until we consider next steps," said a commission spokesman.

The Cairngorms National Park Authority pointed out it was routinely consulted on a variety of works undertaken by the Forestry Commission. "Our approach to these consultations takes into account the effect any proposed work would have on a variety of things such as habitats, known species in the area and public access," said a park spokeswoman.

"There was an incident earlier this year which resulted in the loss of a nest when a contractor did not follow best practice. We were notified about this and have since – with the Forestry Commission – held a seminar especially for forestry contactors on the practicalities of complying with biodiversity obligations to avoid this happening again."