The firm dismissed Nathan Takele following the incident and has repatriated him to Fiji. He flew out of Rarotonga to Auckland on Sunday, and was escorted to the plane by another employee of the company.
Although he is no longer in the country the police and Ministry of Transport investigation into the incident continues and Takele may yet face charges in the Cook Islands.
The 60-foot longliner ended up on the reef off Muri on Friday night, and police have since confirmed that alcohol was a factor in the accident. Takele and other members of the crew were reportedly drunk when the boat struck the reef.
Zambucca was stranded for more than four days until it was finally freed at around 10am on Wednesday with the help of the Layar Mas 291 heavy load carrier and three diggers.
There were fears that the stricken boat could pose an environmental threat to the reef and lagoon, but there was no leak of fuel or oil and the vessel remained intact and was able to be refloated.
After being lifted off the reef it was towed back to Avatiu wharf. It is now expected to be sent to New Zealand for repairs.
The Ministry of Marine Resources has been monitoring the damage caused by the stranding and the efforts to salvage the vessel.
It says most of the damage occurred on the reef flat, where coral, trochus and sea cucumbers have been crushed. But it added that salvage crews had mostly stayed on the same tracks, minimising damage to the habitats