A home affairs public servant has complained to parliament that the department’s whistleblowing scheme is flawed after it failed to independently investigate a report about a staffing incident involving a home affairs senior executive.

The anonymous and heavily redacted submission to the Senate committee examining press freedom states that a public interest disclosure (PID) was made after staff became aware of an issue with hiring practices involving a senior executive within the department in 2017.

But the report was sent back to the department rather than being investigated independently. It is unclear from the submission what ultimately happened with the investigation.

The government has frequently proclaimed the public interest disclosure avenue for government whistleblowers is the proper process for reporting issues rather than leaking to the media.

The home affairs secretary, Michael Pezzullo, has made clear the department would seek to investigate and prosecute public servants who leak sensitive information to the public.

Pezzullo has said officers within the department are trained that they have three options for reporting issues: internal disclosure within the department; to the ombudsman; or to the Australian Commission for Law Enforcement Integrity (Aclei). The submission makes clear the public servant made inquiries with Aclei and went to the ombudsman, but the matter was handled internally.

“A PID report was made to the [Commonwealth] Ombudsman rather than an internal report, obviously given the sensitivity of the information related to [a senior executive],” the unredacted portion of the submission about the incident states.

But the ombudsman referred the matter back to the department, which assigned an executive level 1 (EL1) assistant director to investigate, the submission said. There was no communication with the whistleblower for four months about the investigation.

The submission states it would be a “very courageous EL1 to undertake an investigation which may result in any adverse findings in a matter involving the [senior executive] of the behemoth that is the department of home affairs.”

The submission states that at no time was there any attempt by the department to undertake an independent investigation, and it was a flawed process.

“When reports are made relating to the senior executive service, if the ombudsman is not going to investigate PID reports, there must be seen to be a higher level of independent scrutiny … with ongoing oversight of the ombudsman (or a national integrity commission).”

The public servant, who said in the submission they have more than 30 years in the public sector, said it was “worthy of an episode of ABC’s Utopia” that when leaks like the au pairs saga make it to the media, the AFP is called in by the agency’s department head in home affairs to investigate damaging leaks affecting the minister for home affairs.

The Guardian has contacted home affairs for a response.