The Immigration Department sacked an expert health panel because of fears its members would leak information about Operation Sovereign Borders to the media, government documents reveal.

The 12-member Immigration Health Advisory Group was replaced by a sole adviser, military surgeon Paul Alexander, in December.

The panel, which included psychiatrists, psychologists, trauma experts, nurses and GPs, had been providing independent policy advice to the federal government since 2006.

Documents, obtained under freedom of information laws by AAP, show the secretary of the immigration department, Martin Bowles, was concerned about potential conflicts of interest by members of the panel.

It had become increasingly apparent the contentious nature of some policy approaches in relation to “illegal maritime arrivals” had made it difficult for some members to provide health advice independent of their other interests, he wrote in a ministerial minute.

The conflicts of interest arose from “natural professional interests and obligations” including, in some cases, public and media comment related to issues under consideration by the panel.

“The actual and potential conflicts also present challenges in sharing information on policy and operational activities that are becoming increasingly problematic,” Bowles said.

Because of the creation of a joint agency taskforce, introduction of rapid transfer arrangements and emphasis on expanding offshore processing, it was appropriate to revisit the department’s approach to seeking expert health advice.

Bowles conceded the decision was likely to attract criticism that the department was not interested in frank and impartial health advice.

“This is not the case,” he wrote, referring to Alexander’s appointment and back-up available to him from the department’s chief medical officer and International Health and Medical Services, which provides health care in detention centres.

The Abbott government, in previously defending its decision, argued the panel struggled to provide timely advice in a fast-moving policy environment because of its large membership.

A former panel member, Choong-Siew Yong, from the Australian Medical Association, said the group gave frank clinical advice that sometimes did not fit with government policy.

“Normal confidentiality rules apply in this situation and members respected that,” he said on Thursday. “We thought it was working well and that we were giving high-level, good advice to the department.”

The Greens senator Sarah Hanson-Young said the federal government was worried the panel would not toe the line on immigration and border protection policies.

The government was willing to risk permanently damaging the mental health of asylum seekers and refugees in order to protect its “dirty secrets”, she said.

Comment has been sought from the immigration minister, Scott Morrison.