Environment groups have called for an independent probe into the government’s assessment of an apartment and marina development on protected wetlands in Queensland.

It comes after revelations the former environment minister Josh Frydenberg rejected advice from the environment department that the development was “clearly unacceptable”.

The proposed development by Walker Corporation, which has been a major political party donor, would include more than 3000 apartments, a hotel, shops and marina on Toondah Harbour in Moreton Bay, south east of Brisbane.

The harbour is part of a Ramsar-listed wetland, which is an area that has been declared internationally important under a 1971 intergovernmental treaty that asks members to maintain the ecological character of their listed wetlands.

The Moreton Bay Ramsar includes freshwater lakes, swamps, marshes and sandflats and is an important site for a range of bird species. The development would cover about 40 hectares of this site.

Documents obtained by the Australian Conservation Foundation under freedom of information laws show the department advised the former environment minister on multiple occasions that the Walker Corporation’s development was “clearly unacceptable” due to the impact it would have on “the ecological character of the Moreton Bay Ramsar-listed wetland”.

Frydenberg rejected that advice and sent it to the next stage of the federal assessment process, which is an environmental impact statement.

That process is still under way and no decision on the development has yet been made.

In 2016 the Walker Corporation made a $225,ooo donation to the Liberal party and a $23,000 donation to Queensland Labor, the same financial year in which the initial proposal was submitted for assessment.

Speaking to the ABC on Thursday, Frydenberg said his decision was not an approval of the development but an opportunity for assessment under the Environment Protection and Biodiversity Conservation Act.

He said “it’s got nothing to do with the donor”.

“Under the EPBC Act, the minister has the opportunity to enable his department to undertake a full assessment of the project, and in doing so, get more information, which may lead to mitigation or offsets of any significant environmental impact that the project would have,” he said.

But conservation groups want the process investigated.

“There needs to be an independent probe into this matter. Australians have the right to be confident the natural world is being protected from irresponsible development, especially places as important as the Moreton Bay Ramsar site,” ACF chief executive Kelly O’Shanassy said.

Humane Society International Australia chief executive officer, Erica Martin said it showed the need for new environmental laws in Australia.

“The department was right on the money in saying this proposal should be rejected outright, and it’s disturbing that Minister Frydenberg ignored this advice and opened the door to removing international protections for the sake of development,” she said.

“The Moreton Bay Ramsar site is priceless, and Australia must respect the conventions we’ve committed to.”

The two groups, along with Birdlife Australia, have written the Ramsar secretariat requesting it intervene in the matter and ask the Australian government for an explanation.

“We seek the Secretariat’s urgent intervention on this matter to ensure Australia meets its obligations under the Ramsar convention,” the letter states.

Walker Corporation declined to comment.