Environment campaigners have warned that Scotland will lose vital legal safeguards because ministers have failed to ensure environment and pollution laws will be properly enforced after Brexit.

They said ministers in Edinburgh had refused repeated requests to table new legislation to guarantee citizens and campaigners in Scotland the same rights they now had under European law.

WWF Scotland, the conservation group, said this meant it would be much harder – if the UK left the EU – for campaigners to legally challenge the Scottish government for failing to uphold air quality standards, or to stop wildlife being culled by Scottish Natural Heritage, a government agency, before other dispersal methods were tried.

In an open letter published by the Guardian, many of Scotland’s leading conservation and civic groups have urged Nicola Sturgeon, the first minister, to introduce an environment act guaranteeing that legal rights available within the EU continue after Brexit.

The letter, signed by 16 bodies including the Royal Society for the Protection of Birds, WWF, Scottish Council for Voluntary Organisations, National Trust for Scotland and Royal Scottish Geographic Society, said the climate emergency added to the need for legislation.

Organised by the umbrella group Scottish Environment Link, the letter says: “Nicola Sturgeon has acknowledged that our planet faces a climate emergency. Inextricably linked to this is growing ecological crisis.

“We must not let Brexit derail us from tackling these huge global challenges head on. Whatever the outcome of the current political uncertainties we need robust, binding, targets for the recovery of Scotland’s natural environment, to safeguard both nature and people.”

Its signatories want the new act to create an independent regulator to police government and public agency decisions, and enforce environmental laws to at least the same standard as the EU’s. They also want principles of environmental law used by the EU enshrined in Scots law, and binding targets set to improve and protect the environment.

Under EU law any citizen can go, for free, to the European commission to challenge a government’s or agency’s failure to uphold EU law. The commission can investigate and take enforcement action, including taking the member state to the European court of justice.

Those powers have been used at EU level by the legal group Client Earth to make the UK enforce air pollution regulations; by the RSPB to halt a cull of barnacle geese on Islay, sanctioned by Scottish Natural Heritage; and again by the RSPB, to protect peatlands in England.

Michael Gove, the UK environment secretary, is planning to introduce similar procedures after Brexit to cover environmental legal enforcement in England. The Labour-run Welsh government, which like Holyrood has devolved responsibilities for the environment, is involved in that process.

Although the UK, Scottish and Welsh governments have cooperated closely on measures to transpose EU environment regulation into UK and Scots law, ministers in Edinburgh have refused to cooperate with Gove’s plans for new regulatory measures. So the Scottish government’s own expert advisory panel and the Royal Society of Edinburgh, Scotland’s national academy, have urged ministers to set up the independent regulator, as sought by the letter’s signatories.

Roseanna Cunningham, the Scottish environment secretary, responded to the letter by insisting her government was committed to matching or exceeding the EU’s environment laws, but she refused to confirm it would introduce a new environment act or oversight agency.

She said: “While our choice would be to remain fully within EU governance systems our approach will ensure we remain true to the EU environmental principles and ensure governance that fit Scottish needs, circumstances and ambitions. I welcome the continuing involvement of environmental NGOs and civil society in Scotland in this work.”

Lang Banks, the director of WWF Scotland, said: “Citizens have a right to raise concerns but we now risk losing the ability to freely access environmental justice. We are in a climate emergency, we’re in the midst of a biodiversity crisis, and this is the point where we need to be ramping up our environmental protections. Brexit means we risk losing the protections we currently have, when we need them most.”

• This article was amended on 27 June 2019. An earlier version referred to a legal process to stop wildlife being “inhumanely culled” by Scottish National Heritage. The word “inhumanely” has been removed, and text added to more accurately reflect the situation.