Federal Environment Minister Melissa Price has appointed one of her former advisers to the position of chief executive of the Great Barrier Reef Marine Park Authority.

Key points: Josh Thomas is a former adviser to Ms Price and her predecessors Josh Frydenberg and Greg Hunt

Josh Thomas is a former adviser to Ms Price and her predecessors Josh Frydenberg and Greg Hunt Ms Price insists Mr Thomas's appointment went through a "merit-based selection process"

Ms Price insists Mr Thomas's appointment went through a "merit-based selection process" Key environment groups say there were not consulted on the appointment

The appointment comes following a governance crisis at the Authority in which a director left following revelations she was profiting from funds handed out by the Authority.

It also comes after the political decision to award $444 million to the small charity, the Great Barrier Reef Foundation, was subject to widespread criticism.

Josh Thomas was on staff at the Department of Environment until the Coalition came to power in 2013, when he moved to become an adviser to Greg Hunt when he became environment minister.

Mr Thomas continued to work for each subsequent environment minister — Josh Frydenberg and then Ms Price.

"Mr Thomas brings a strong understanding of the Authority with more than 15 years' experience in the public and private sector and has academic qualifications in science and international affairs," Ms Price said in a statement.

The Authority says Mr Thomas has "helped shape and lead environmental policy and programs for the Great Barrier Reef and in terrestrial natural resource management".

It noted he had "worked in a number of senior public sector roles and across the environment, agriculture and finance portfolios."

The Great Barrier Reef Authority also put out a statement announcing the appointment.

"Mr Thomas is committed to enhancing Australia's natural environment and has been a strong advocate for incorporating both contemporary science and Indigenous traditional knowledge into environmental management throughout his career," the Authority's statement said.

Ms Price's office said a panel put forward a shortlist of candidates to the Minister, and the Authority had input into that shortlist.

The Minister's office said Mr Thomas was on the shortlist for the role.

"The merit-based selection process was conducted by a public service panel and was endorsed by the Australian Public Service Commissioner," Ms Price said in her statement.

The statement failed to cite Mr Thomas's employment in her office, but said his "application received widespread support from non-government organisations and environmental groups".

Labor says appointment is nepotism

Key environment groups, WWF, Australian Marine Conservation Society and the Australian Conservation Council all said they were not consulted.

"Now more than ever the Authority needs strong, bold and independent leadership," said Imogen Zethovan from the Australian Marine Conservation Society.

"The Great Barrier Reef isn't just a unique global icon, but it's also the cornerstone of Australia's $31 billion marine tourism industry."

Ms Price's office told the ABC that Mr Thomas's application for the position came with 10 recommendations from a range of groups including environmental non-government organisations.

Labor's environment spokesman Tony Burke said the move was nepotistic.

"The same Government that won't give workers a pay rise will give salaries of more than 300k a year to anyone who has ever been associated with the Liberal Party," he said.

"This is not only about the Marine Park Authority — it's about what this entire Government has become.

"We no longer have a Government, we've got a club."

The Government has previously been criticised by Labor for appointing a string of people linked to the Coalition to lucrative diplomatic positions, as well as to quasi-judicial positions on the Administrative Appeals Tribunal.