MNZ alleges Atkinson was the skipper of the 13m fishing trawler Debbie Jane when it ran aground on Waimairi Beach in December 2019.
News reports at the time said that Atkinson and two crew members were rescued and were treated in hospital for hypothermia.
Atkinson's lawyer, Michael Starling, told the Christchurch court last month that Atkinson's phone had been disconnected and that a letter couriered to his last known address had been returned unopened.
Atkinson said today he had lost his phone, then changed his number, but he indicated he had not been trying to evade justice.
"I've been here all the time. I haven't been hiding. I live on a yacht over at West Shore [Napier]," he said.
However, he had not yet managed to talk to Starling about the case.
Judge Cooper remanded Atkinson on bail to appear in the Napier District Court on May 18.
He also advised him to get in touch with his lawyer.
The warrant to arrest was cancelled.