The Senate estimates process on Operation Sovereign Borders has failed and Senator Stephen Conroy has paid the price for his political miscalculation, writes Michael Brissenden.

Labor's defence spokesman Stephen Conroy has accused the Federal Government of hiding behind the military as it attempts to keep operational matters related to Operation Sovereign Borders (OSB) secret.

Senator Conroy's handling of the politics surrounding the increasingly partisan issue might now be in question after his accusation that the general in command of the operation, Angus Campbell, was part of a "political cover-up". But it is clear that in this case the Senate estimates process, designed to solicit information from government and bureaucracy, has failed.

The Government will ride Senator Conroy's political miscalculation for all it's worth but it remains determined not to give away anything that might be linked to what are now referred to as "on-water operational matters".

At times the Senate estimates process became an absurdist parody that would have made Samuel Beckett proud.

Take the subject of the orange lifeboats as Act One.

On Tuesday, Customs and Border Protection CEO Michael Pezzullo confirmed the Government had spent $2.5 million on orange lifeboats - the same lifeboats that have washed up on Indonesian shores full of asylum seekers.

Their stories have been widely reported and we have seen vision of the boats being towed by the Triton, an Australian Customs ship engaged in OSB.

Mr Pezzullo would not confirm how many of the orange lifeboats the Government had bought or how much each one cost, but he did confirm they would buy more if needed.

But under questioning from Senator Conroy yesterday, Defence Force chief General David Hurley would not confirm the boats had even been received.

"That's an on-water issue," he said.

What flag do they travel under, Senator Conroy asked. Do they become Australian flagged?

"We can't comment on on-water matters," General Hurley said.

So are they Navy assets?

General Hurley would not confirm the orange boats were being used in OSB but nonetheless also would not confirm they were even Navy assets.

"They are on-water issues," he said.

What about the vision - widely aired on Australian TV, including on the ABC - showing an orange boat being towed by the Triton?

Senator Conroy directed his question to Defence Department head Dennis Richardson.

Senator Conroy: "The vision is on YouTube."

Mr Richardson: "Well I don't care what it's on. We're not commenting on it."

Senator Conroy: "But what I'm confused about is the Prime Minster has stated publicly that we don't have a tow backs policy. I'm trying to understand what the Navy are doing there."

Mr Richardson: "What is on the public record is on the public record. We have nothing to add."

What about general training? Has there been any new training put in place for Navy personnel?

Chief of Navy Vice Admiral Ray Griggs told the committee he could not talk about it.

"If I talk about the type of training then I'd be going into on-water matters and the techniques and procedures that may be used on water," he said.

Senator Conroy, clearly frustrated, said: "It seems a little silly that you are unable to provide the simplest of answers about the officers and personnel under your command."

The matter of exactly how far Australian Customs and naval ships ventured into Indonesian waters was also a matter of "on-water operations".

Senator Conroy now finds himself under considerable political pressure for his attack on General Angus Campbell.

In the committee room on Tuesday he withdrew his comments for the Hansard record but Government ministers lined up all day yesterday to demand an apology.

The House of Representatives passed a motion "admonishing" Senator Conroy.

And although he now says he has no criticism whatsoever of service personnel carrying out government orders, by accusing the military of being part of a "political cover-up", the politics has become stuck in a chest-beating argument about patriotism and Senator Conroy has given the Government the distraction it needed.

Michael Brissenden is the ABC's defence correspondent based in Canberra. View his full profile here.