THE captain of the coal carrier dubbed the "Death Ship", who has sold guns and attacked a crew member, was known to Australian authorities for almost 18 years before two men died on board his vessel.

The Department of Border Protection has been forced to defend its monitoring of foreign sailors after former MV Sage Sagittarius master Venancio Salas Jr was discovered captaining a ship at the Port of Gladstone in February by Australian Regional Media.

Capt Salas had been wanted for questioning by the New South Wales Coroner into how two Filipino nationals died aboard the ship as it approached Australia in late 2012.

The deaths have been described by investigators as "highly suspicious".

The revelation of Capt Salas's location led to a subpoena being issued to appear at the NSW coronial inquest.

A Senate Inquiry into foreign shipping asked Border Protection officers to explain how the captain - who has previously confessed to selling guns and assaulting a gay crewman - was able to return to Australian seemingly unnoticed.

Queensland Nationals Senator Barry O'Sullivan asked the Department in March: " who is moving in our waters? Did you have a file or not?"

Border Protection confirmed it had "holdings" on Capt Salas since December 24, 1994 - 17 years and eight months before a spate of fatalities occurred on the Sagittarius, now known as the "Death Ship".

"These holdings relate to a range of interactions the department has had with Mr Salas and information we have received about his activities and movements," the department wrote in response to a question on notice.

A Border Protection spokesman told ARM that authorities had boarded the Sagittarius "on a number of occasions".

Officers also boarded Capt Salas's new ship - the Kypros Sea - at a Northern Territory port on January 21 2016.

The department did not pass on news of Capt Salas's return, apparently unaware he was wanted for questioning by the inquest examining the deaths aboard the Sagittarius.

Officers confirmed they had no intention of stopping Capt Salas from leaving the country in February 2016 until a subpoena was issued by the NSW Coroner.

In a separate response, the department wrote that Capt Salas was not marked for an "alert" by Border Protection, because his sale of guns on board a ship bound for Australia may not have been illegal.

The legality of selling guns on board was murky enough for Capt Salas to ask the Coroner to grant him immunity from prosecution when he appeared at the inquest in May last year.

Senator O'Sullivan said he was now seeking further information from the department.

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