More than 5,000 of England’s most sensitive, rare and protected natural habitats are at high risk of being destroyed by development under Labour’s new planning bill, according to legal analysis of the legislation.

The Guardian has examined the threat the bill poses to 5,251 areas known as nature’s “jewels in the crown”, as some of the country’s most respected wildlife charities call for a key part of the bill to be scrapped.

The areas at risk from Labour’s planning changes include cherished landscapes such as the New Forest, the Surrey heaths, the Peak District moors, and the Forest of Bowland.

Rivers such as the Itchen in Hampshire and the Wensum in Norfolk are also threatened by the bill. The thousands of protected habitats are locations for threatened British wildlife such as nightingales, badgers, dormice, otters, butterflies, dragonflies, kingfishers, tufted ducks and egrets.

The bill is the product of the government’s promiseto build 1.5m homes to help address the UK’s housing affordability crisis, and approve 150 major infrastructure projects, in this parliament. The pledge is key to Labour’s plan to boost economic growth; however, a recent study suggests the government is likely to miss its new homes target. The government says the bill does not weaken environmental protections.

But according to three separate legal opinions on the planning and infrastructure bill currently going through parliament, legal protections will be rolled back by the legislation, making it easier for developers to build on areas that have historically been protected under UK and international law.

The Guardian has identified 10 protected sites that are under particular threat from development under the new legislation amid growing criticism of Labour’s bill.

They include one of the last strongholds for nightingales in England at Lodge Hill in Kent; a wetland dating back 2,600 years in south Devon; an internationally important tidal wetland at Tipner west in Portsmouth; and woods dating back as far as the 17th century at Sittingbourne, Kent, part of the 2.5% of the UK’s ancient woodland that still remains.

These areas represent just a handful of the most protected environmental gems across England which include 4,100 sites of special scientific interest (SSSIs), all currently protected by the Wildlife and Countryside Act 1981; 71 wetlands protected under the internationally-binding Ramsar convention; 256 special areas of conservation (SACs) and 824 special protection areas, (SPAs) all protected under UK and international law in the habitats directive.

Though numerous, these protected areas in total only cover just under 8% of land in England. Critics of the bill say ensuring they continue to be protected does not amount to a block on building new houses.

In a legal opinion, Alex Goodman KC said the consequences of the planning and infrastructure bill as drafted were that any adverse impacts a development inflicted on the most protected natural areas in England, including SSSIs, SACs and Ramsar sites, must be “disregarded”.

“[The bill] thereby withdraws the principal legal safeguard for protected sites,” he said. “This amounts to a very significant change.”

Goodman has provided one of three separate legal opinions on the bill since it was presented by Angela Rayner, secretary of state for housing, communities and local government.

All, including that of the government’s own watchdog, the Office for Environmental Protection (OEP), challenge Rayner’s assertion to parliament that the bill is not a rollback of environmental law. Rayner has been threatened with a judicial review brought by nature groups if she does not “correct” her comments.

Goodman said: “The only possible reading is that the bill will have the effect of reducing the level of environmental protection provided.”

Glenys Stacey, chair of the OEP, said: “The bill would have the effect of reducing the level of environmental protection provided for by existing environmental law. As drafted, the provisions are a regression.”

Key concerns focus on part three of the bill, which provides a mechanism for developers to sidestep current environmental obligations by paying into a nature restoration fund, which will be used at a later date to create environmental improvements elsewhere.

Once the fee is paid, the development can go ahead even if it “inflicts adverse effects on the integrity of a protected site”. Dubbed a mechanism to pay “cash to trash”, the bill contains no requirement for developers to measure what harms are taking place during the planning process. Irreplaceable habitats have no extra protection from development.

Leading charities have called for this section to be scrapped entirely.

Dr Ruth Tingay, co-director of Wild Justice, said the government seemed intent on causing unrecoverable damage.

“Imagine flattening an irreplaceable grade I listed building like the Royal Albert Hall, replacing it with karaoke machines in various towns and then telling the public this is a ‘win-win’ for architecture and music. Swap the Royal Albert Hall for any one of the UK’s nationally important and protected habitats, swap the karaoke machines for a few pathetic tree-planting schemes, then tell people this is a ‘win-win’ for the environment and the public, and the analogy is brutally clear.”

David Elvin KC, in a third legal opinion, said part three of the bill was regressive and potentially in breach of international law.

Ellie Chowns, a Green MP, said there was a serious legal question with the bill because although the secretary of state asserted to MPs there was no reduction in environmental protections, the reality of the legislation was that the bill was in fact a rollback of environmental protections.

“We have a responsibility to protect the most important, the rarest and most in need habitats, like chalk streams, ancient woodlands, peat bogs; these jewels in the crown of our ecological heritage have their protections weakened in this bill,” she said. “These are irreplaceable habitats, which by their very nature cannot be created anywhere else in some kind of compensation schedule.”

A government spokesperson said: “We completely reject these claims, and have been clear that our planning and infrastructure will not weaken environmental protections.

“The government has inherited a failing system that has delayed new homes and infrastructure while doing nothing for nature’s recovery.

“That’s why we will deliver a win-win for the economy and nature as part of our Plan for Change, unblocking building and economic growth while delivering meaningful environmental improvements.”