Operational orders that resulted in Australian border protection boats conducting unlawful incursions into Indonesian waters are still current today, the head of Operation Sovereign Borders said during cross examination in a freedom of information case with Guardian Australia.

He also revealed that Operation Sovereign Borders had orders allowing officers to board vessels outside Australian waters.

Major General Andrew Bottrell, the head of Operation Sovereign Borders, came under intense legal questioning at the administrative appeals tribunal in Sydney on Monday, fighting to keep documents relating to asylum seeker boat turnbacks secret.

The case concerns access to government orders to execute turnback operations in 2013 and early 2014, including those involved in Australia’s unlawful incursions into Indonesian waters. It is part of a long-running freedom of information case initiated by Guardian Australia journalist Paul Farrell.

The Department of Immigration and Border Protection is arguing that release of the documents would threaten the Australia’s national security. But in the first few moments of the hearing on Monday, it was revealed the department had accidentally handed over some of the very documents it was seeking to prevent Guardian Australia obtaining.

Guardian Australia’s barrister, Tom Brennan, sought to test whether some of the documents were no longer “current”, meaning their disclosure would not affect existing operations.

Brennan suggested to Bottrell that two operational orders that resulted in those incursions were no longer current.

Bottrell responded that in fact they were still current.

Brennan also sought to determine whether boarding an asylum seeker vessel that was in the territorial waters of another country was lawful and permitted under Operation Sovereign Borders. If not, it would have undermined the department’s case for keeping the documents about those actions a secret.

Brennan said: “I want to suggest to you that in January 2017, that absent a rescue situation, in Operation Sovereign Borders, [boarding a vessel] could only occur in international or our territorial seas.”

Bottrell responded: “No that’s not the case,” indicating that operational orders allowed for boat turnbacks to occur inside the territorial waters of other countries.

Much of the rest of the questioning sought to establish that the information that could be gleaned from ship logs or operation manuals for Operation Sovereign Borders, could be gleaned from information already in the public domain.

One example discussed was a Guardian Australia’s report in April 2014 revealing the extent of some of the incursions into Indonesian waters.

Under questioning from Brennan, Bottrell argued that report was detrimental to national security. In particular, he said revealing the name of one of the border patrol boats used, as well as their distance from Indonesia was detrimental “People smugglers would have gleaned … what sort of capability was used,” Bottrell said.

That was despite other questioning revealing that many similar details were published on government websites, including details of the boat’s locations and activities, as well as information about the boats’ ranges and top speeds.

Bottrell responded that the capabilities of the vessels in general, was different to their capability in the context of particular operations.

The case is also likely to determine whether national security can be invoked to conceal documents relating to people smuggling ventures.

Brennan told the tribunal: “There can be no doubt that people smuggling activities are a matter of significant public interest ... but they are not in my submissions ones that rise as high as touching the security of the commonwealth.”

The hearing was scheduled to continue on Tuesday.