The dry dock facility is inside a military-controlled base. Everyone on the site were saliva tested everyday.
While they were there in Sydney, the crew remained on the vessel, working on maintenance and servicing, Rushbrook said.
PPE and physical separation between workers were used to minimise Covid-19 risk between the crew and the Sydney-based contractors working on the ship, he said.
"The Aratere crew had a standard Covid-19 test before leaving Sydney, and again on arrival in Wellington on Thursday. They have since been tested again. All the tests have been negative", Rushbrook said
KiwiRail followed Health Ministry advice and instructions at all stages, he said.
The Ministry has been approached for comment.
The Aratere was out of action at the same time as the Kaiarahi ferry, which was out of service due to problems with her gearbox.
The situation left KiwiRail with only one Interislander ferry operating for 10 days during September.
KiwiRail Chief Operations Officer Todd Moyle said at the time it was unlucky and an unprecedented situation.
"While it's fortunate that this disruption has not coincided with our peak freight season, New Zealand's supply chain faces a challenging few weeks as we manage freight volumes across Cook Strait in a constrained manner."