The NSW Greens have lost a bid to kill off 'Operation Prospect' — the NSW ombudsman's long-awaited investigation into the improper surveillance of senior police officers.

Greens MLC David Shoebridge said the investigation had turned into an "unholy mess" when he moved amendments in the NSW Upper House last night that would have suppressed the ombudsman's final report.

"The Government created [this] monster ... and it should now kill it off," he said.

"It has turned from an investigation of the original police bugging, the scandal of Supreme Court judges rubber-stamping intercept warrants, rubber-stamping listening device warrants, without any capacity to review them.

"It has turned from an investigation of that appalling conduct to an investigation of the whistle blowers and, worse still, to an investigation of some senior police."

Mr Shoebridge called for all records relating to Operation Prospect to be handed to the NSW Crime Commission, where they would effectively be embargoed for 10 years.

He moved the amendments during a debate on legislation to establish the Law Enforcement Conduct Commission, which was ultimately passed.

Operation Prospect was set up in October 2012 when the State Government granted the NSW ombudsman special powers to investigate the surveillance of more than 100 police officers between 1999 and 2001.

That surveillance was carried out under Operation Mascot/Florida, an internal-affairs investigation into police corruption involving Deputy Commissioner Catherine Burn and headed by Police Commissioner Andrew Scipione.

Investigation 'a piece of garbage'

Shooters and Fishers MP Robert Brown backed Mr Shoebridge's bid to kill off Operation Prospect, calling it "a piece of garbage".

"The amendments seem a little counter-intuitive," he said.

"[But] if the amendments have the effect of enabling the Legislative Council to now draw a line under all those occurrences and perhaps save some of the people involved from a bit more pain, surely that is the compassionate thing ... to do."

But the Government, Labor and Christian Democrat MP Fred Nile combined to defeat the amendments.

"It is basically an amendment designed to gag or to provide secrecy," Mr Nile said.

Operation Prospect could face legal challenge

The Greens are not the only threat to the future of Operation Prospect.

The head of the NSW Crime Commission threatened to seek a Supreme Court injunction prohibiting the release of the ombudsman's report.

Peter Hastings QC accused the investigation of "cherry picking" evidence and lacking "procedural fairness" when he wrote to the acting ombudsman Professor John McMillan last month.

In a letter obtained by the ABC, Mr Hastings said, "I have endeavoured to ensure that you have received the maximum cooperation from Commission staff in responding to requests for information and documentation."

"But this has not been reciprocated and, not withstanding the numerous complaints, nothing has been done to redress the unfairness in the processes adopted," he wrote.

Mr Hastings indicated both Deputy Commissioner Burn and former Deputy Commissioner Nick Kaldas also had concerns about the investigation.

"It is a matter of public record that former Deputy Commissioner Nick Kaldas has serious complaints about the manner in which the investigation has been conducted, albeit with a different emphasis.

"It is significant that those senior personnel who have been investigated, but who have different interests, have major grievances about the way in which they have been treated."

NSW Crime Commission spokesman, Assistant Commissioner Peter Dein, would not comment on the letter but said Mr Hastings regularly wrote to the ombudsman's office.

"The Crime Commissioner has written to the ombudsman on a number of occasions in relation to procedural matters," he said.

A spokeswoman for the NSW ombudsman said the report into Operation Prospect was expected to be handed to Parliament before the end of the year.