Australia is unable to continuously track all its naval vessels, the commanding officer of Operation Sovereign Borders (OSB) has told a Senate inquiry into six “inadvertent” incursions into Indonesian waters.

In the hearing before the foreign affairs, defence and trade committee on Friday, examining the circumstance of the incursions, senior OSB personnel, including Lieutenant General Angus Campbell, conceded that officers commanding the civilian policy were not aware where vessels were at all times.

A report produced by defence and customs into the incursions, a version of which was made public in February, concluded that every case was in breach of instructions and due to “miscalculations” of Indonesia’s boundaries by naval crews.

Questioned by Labor senators Stephen Conroy and the committee chairman Sam Dastyari, Campbell and Rear Admiral Mike Noonan, commander of border protection, conceded that their ability to track vessels was “not uniformly continuous”.

The responses appeared to refer directly to Operation Sovereign Borders, but the immigration department secretary, Martin Bowles, later interjected to clarify that they were meant as general responses to operational matters.

Asked whether vessels used by OSB ever switched off their location devices, the panel declined to answer, citing operational sensitivity.

Noonan said earlier that OSB had three command venues with the capacity to monitor assets, one in Darwin, one in Canberra and one in Bungendore, New South Wales.

Campbell said his and Noonan’s offices in Canberra were just one floor below the Australian Maritime Security Operations Centre (Amsoc), which contains a watch floor where ships could be monitored.

Noonan said that at no point during the six incursions was he present on the watch floor. He later said “operational reports” containing “positional information” would be filed from naval vessels every four to six hours.

“It is rare for me to go onto the watch floor unless it is a loss of life situation,” Noonan said.

Immediately after Noonan made those remarks, Michael Pezzullo, the chief executive of Australian Customs and Border Protection, said Noonan did not need to go into details of where he was at the time of the incursions.

In a rare break from public interest immunity, which allowed many of the panel to decline to answer questions, Campbell told the committee that no ships had opened fire on asylum boats during OSB operations.

“Are we shooting? No we’re not, senator,” Campbell said in response to a question from the Greens immigration spokeswoman Sarah Hanson-Young.

Bowles later cited public interest immunity in declining to answer whether naval vessels had turned off their lights during the incursions.

Pezzullo said inquiries into the conduct of individual naval officers involved in the incursions were underway.

The committee hearing continues.