A logging operation at Poland’s spectacular 55-mile-long Vistula lagoon is casting a “dark omen” of deforestation and biodiversity collapse across Europe’s forests, campaigners say.

Tree felling around the Natura 2000 site is aimed at clearing a path to the Baltic Sea for use by Poland’s navy, to the alarm of Russia. But they are just one front in what some academics describe as a war on nature.

Campaigners blame the EU’s own use of biomass to meet most of its renewable energy goals for encouraging logging in Europe’s virgin forests.

The EU expects to lose about 125m tonnes of carbon sequestration potential from forests between 2010 and 2030, with countries such as Estonia, Latvia and Austria transforming from carbon sinks to carbon sources.

Poland still hopes to clear swathes of the Białowieża Forest, and several other ancient woodlands are also under threat across central and eastern Europe, with potential effects on Europe’s greenhouse gas emissions.

“First Białowieża, now [the] Vistula lagoon,” said Adrian Bebb, a campaigner for Friends of the Earth. “The Polish government is once again ignoring its citizens and trying to destroy an irreplaceable protected area. With biodiversity threatening to collapse, illegal logging rampant and authoritarianism on the rise, allowing this shipping channel to pass would be a dark omen for the future of Europe.”

The European commission is thought to have rebuked Poland in a technical meeting on Friday for the construction, which may breach environmental risk assessment laws.

The Polish environment ministry did not respond to requests for comment.

Hannah Mowat, a spokeswoman for the forest protection group Fern, said. “The biggest factor in the destruction [is] incentives given by the EU to burn trees for energy. It is urgent that the criteria determining which wood countries can burn is revised, to ensure that we do not obliterate what’s left of our natural inheritance.”

Illegal logging is another cause of deforestation, especially in countries such as Romania, where rampant timber crime has pushed some of Europe’s largest remaining primeval forests to the brink.

Andrei Ciurcanu, a spokesman for the Romanian NGO Agent Green, said that government figures, seen by the Guardian, showed that 38m cubic metres of wood were harvested in the country last year – more than twice as much as officially claimed.

“Old-growth forests in our national parks are being massively logged,” he said. “It is an environmental catastrophe taking place in front of the EU’s eyes.”

The country’s renewable energy plans for 2030 project a 55% increase in demand for domestic wood for bioenergy in the intervening years.

Poland’s clean energy plan similarly says that bioenergy has “the largest potential” for achieving its renewable energy target.

With 80% of EU forests already in a poor conservation state, the Center for Climate Integrity will on Monday launch what it calls a “landmark” court action against the EU.

The lawsuit demands that bioenergy be removed from consideration as a renewable energy source for meeting the EU’s 2030 targets.

A European commission spokesperson said: “We tabled a comprehensive policy framework aimed at guaranteeing the sustainable development of bioenergy, while at the same time enhancing the role of land and forests as carbon sinks and incentivising their productive and sustainable use. This approach was confirmed by the co-legislators – the member states and the European parliament – when adopting the directive last year.”