David Atkinson, who was allegedly skippering the boat when it became marooned, has been charged with operating a ship and causing danger and risk, as well as exposing individuals to risk of harm or illness.
The boat's owner, Jeremy Hatherly, and his company Hatherly Fishing Ltd, have also been charged.
They are all due to appear at Christchurch District Court on February 17.
A court staff member confirmed today that no pleas have yet been entered.
Atkinson and two crew members were rescued after the beaching and were treated in hospital for hypothermia.