Australia on Friday denied fresh claims of asylum-seeker abuse by its navy as "completely unsubstantiated" while confirming for the first time that it was turning boats back to Indonesia.

Immigration Minister Scott Morrison broke with months of secrecy over the government's military-led Operation Sovereign Borders people-smuggling crackdown to concede that boats were being turned around.

"It is the policy and practice of this government to intercept any vessel that is seeking to illegally enter our waters and where safe to do so, remove it beyond Australia's waters and contiguous zone," Morrison told a Senate inquiry.

He has previously refused to confirm or deny turn-backs for operational security reasons.

The minister would not confirm how many boats had been turned back but said "none shall pass is our objective".

The head of the military operation, Lieutenant-General Angus Campbell, said a total of 22 boats carrying 1,106 asylum-seekers had arrived since September 18 last year.

But none have made it to Australia since December 19 -- the first time in six years that January has passed without a single boat arrival.

Morrison would not comment on whether confirmation of the policy, which has angered Jakarta, would increase tensions with Australia's strategic neighbour.

"Australia respects Indonesia's sovereignty and we respect the environment in which the government of Indonesia operates domestically, as they do the Australian government our own domestic environment," he said.

Indonesia relations 'tense'

Relations with Jakarta have been strained since a phone-tapping row late last year, with recent revelations that the navy strayed into Indonesian waters during asylum-seeker operations further testing ties.

Morrison said the "tense environment" with Jakarta was "not of this government's making" and "further commentary in the public domain about these sensitive operational matters doesn't assist that process".

Both Morrison and Campbell defended the clandestine nature of the mission, with the immigration minister saying further disclosures "would prejudice current and future operations".

"It would put people at risk who are involved in our operations and unnecessarily cause damage to Australia's national security, defence and international relations," he added.

Campbell said some of Australia's partner governments would prefer that matters were handled "discreetly and quietly, cooperatively ... behind the scenes".

He argued against the release of documents about the operation to the Senate, saying they "may impact upon Australia's relations with foreign states and damage those relationships".

Campbell called for unified support for the operation, saying both people-smugglers and their clients "would hope to hear a stark divergence of views in the public debate in Australia that may reinforce a persistent, but incorrect, assumption by them that Australian policies will change".

The remarks came as fresh claims of mistreatment emerged from asylum-seekers turned back to Indonesia by Australia's navy.

Somali asylum-seeker Boby Nooris told the Australian Broadcasting Corporation he was sprayed in the eyes by officers, feeling "pain like chillies" which temporarily blinded him and caused him to stumble into an engine pipe, burning his hand.

Morrison said navy personnel carried "personal defensive devices" but said they were used "in accordance with their training and in accordance with strict guidelines."

"Any suggestion of mistreatment or misuse of force or misuse of any of these devices that are available to them is completely unsubstantiated, completely without basis and is rejected by the government," he said.

"We are not running a welcoming service out there. We are not running some sort of welcoming committee," added Morrison.

"What we are doing is implementing a policy which is strong, which can be tough."

Hundreds of asylum-seekers have died making the dangerous sea voyage from Indonesia to Australia in recent years, prompting the so-called Sovereign Borders crackdown.