Wildlife is disappearing at an unprecedented rate in the countryside but nature is compensating as more species colonise urban areas, the government's ecological advisers say.

In the 12 years to 2006, the overall population of urban birds increased by 14%. Pigeon numbers more than doubled, and there were big increases among green woodpeckers, goldfinches, robins and great tits.

Natural England's annual state of the natural environment report, published today, finds birds, bees and other insects deserting intensively farmed lowland areas for better conditions in urban gardens and on brownfield land, which is relatively undisturbed and therefore safer for them.

Some butterfly species, it says, are now more likely to be found in suburban areas than in the countryside, and at least 40 species of invertebrates are now wholly confined to towns.

Some creatures seem to be adapting specifically to new developments, says the report. More than half of the summer roosts of some species of bat are in man-made structures less than 30 years old.

But while man-made habitats now make a large contribution to the maintenance of UK wildlife diversity, there are immense and growing problems elsewhere.

"Our land and seas are under more pressure than ever before," says the report. "We have a growing population with growing aspirations, meaning increasing demand on the natural environment to provide food, energy, leisure and space for development.

"We are now locked into at least 50 years of unavoidable climate change. Wildlife is increasingly isolated in protected areas, unable to move with the changing climate.

"The current system of conservation has often focused on protected areas such as sites of special scientific interest and national parks. But away from these areas the natural environment is increasingly under threat. It not well placed to withstand the challenges of development and climate change."

Yesterday the agency was backed by all Britain's leading environment groups, including the National Trust, the Campaign to Protect Rural England and the Royal Society for the Protection of Birds as it called for a radical new approach to conservation to match the unprecedented scale and speed of the habitat change taking place in the countryside.

In a barely veiled criticism of the government's infrastructure plans, the report argues that bureaucrats should work with nature and not against it when planning roads and airports, flood defences and major developments including housing, ports, wind power and potential tidal barrages.

"We need a new, more dynamic approach to conservation that allows nature to adapt ... and reconnects people with the natural world," it said.

Dr Sue Armstrong-Brown, the RSPB's head of countryside conservation, said: "We are seeing the consequences of decades of ignoring environmental limits. Now, with the climate changing and wildlife crashing worldwide, it is time for a new green leadership.

"There has never been a time when human action has put so much wildlife in peril. The government should support Natural England's plans and allocate enough money to put them into place."

Matt Shardlow, the director of the invertebrate conservation trust Buglife, said: "Dire disintegration of wildlife habitats combined with poor management of the remaining fragments has caused a conservation 'crunch' that has left wildlife, and particularly the little animals, in a right state."

At a glance

Positive trends

· 10% of landscape has been enhanced in last 10 years

· Big increases in heathland and wetland bird populations

· More access to countryside

· Otter recovery continues, red kite now common

Negative trends

· 20% of landscapes show neglect

· Rivers and lakes in poor condition

· Woodland birds, bumblebees and some butterflies in decline

· Many wading birds in decline