The maritime union says the transport department is either incompetent or deliberately misled a Senate committee after evidence about the MV Portland was corrected.
The government issued Alcoa with a temporary licence in October 2015 to use a foreign-flagged ship.
At 1am on January 13, five crew aboard the Alcoa-owned ship the MV Portland were pulled from their beds by security guards and escorted off the ship.
Five foreign replacement crew were then escorted aboard to join 12 remaining Australian crew, who were not union members and not involved in the protest, so that the carrier could set sail for Singapore.
The Portland had carried alumina between Western Australia and Victoria for more than 27 years.
Two senior transport department officials told a Senate estimates hearing on February 8 a document with written reasons as to why the temporary licence was granted to Alcoa had been tendered in court.
But the department's deputy secretary Judith Zielke wrote to the committee this week to correct this evidence.
"I wish to advise that no document identifying the reasons for the decision to grant a temporary licence to Alcoa in October 2015 was produced or tendered in court," she wrote.
Maritime Union national secretary Paddy Crumlin said the government needed to explain how the error occurred.
"This means the department of transport is either highly incompetent or deliberately misled the Senate committee," he said in a statement.
Alcoa Australia said in January the sale of the MV Portland protected 700 jobs at the Portland smelter, with more than $6 million a year in savings to the company.
It claimed the ship had been held hostage by the union for two months.
The committee also heard the company advised the department on January 12 as to what action was being taken in regard to the Portland, including the use of security officers.
A departmental executive officer also contacted Employment Minister Michaelia Cash's office.
