Talley's staff continued to liaise with Carlaw and Stokes to check on the welfare of Stokes and his family.
But their lie was soon uncovered and they were charged with deception, causing a loss of $173,650 to Talley's Fisheries.
Carlaw told police she lied because she was trying to help her partner as she had "real concerns for his wellbeing if he stayed on the boat".
Stokes and Carlaw, who now live in Christchurch, pleaded guilty earlier and were sentenced at Christchurch District Court today.
The amount of loss was calculated at costing the company $4000 an hour, Judge John Macdonald was told, taking into account the running costs of the ship, including wages and fuel, as well as the loss of fishing time.
The judge said he found the numbers "extraordinary".
Stokes' defence counsel, Craig Ruane, said a cheaper option for the company would've been to drop Stokes off at the Chathams and get him flown back to the mainland for there.
But he accepted that Talleys took Stokes' claims at face value - a "humanitarian issue which turns out to be very expensive".
Police prosecutor sergeant Paul Scott said the fishing company took the safest option in returning to port.
Scott said that if Stokes had gone to the ship's captain and said he didn't want to work on the ship anymore, he would've been put ashore at the next opportunity.
Stokes is now working as a security doorman and already paying off fines at the rate of $20 per week. He could pay another $25 on top of his fines back to the company as reparation, Ruane said, but accepted it was a "token gesture but at least better than nothing".
Defence counsel Sunny Teki-Clark said Carlaw was not in full-time employment, and also paying back fines.
She was "very remorseful", he said, and only "just followed on with what appears to be Mr Stokes' idea".
"She was concerned for his wellbeing. It was around the Christmas period. She didn't think about the very serious consequences her actions were likely to have," Teki-Clarke said.
Judge Macdonald said if she had only been honest, it would've "put an end to the lie then and there".
"The case is clearly unusual. I've not heard of a case like this before," the judge said.
Judge Macdonald found Carlaw's culpability as being less than her partner and sentenced her to 200 hours of community work. He also ordered her to pay reparation of $3000 at a rate of $30 per week.
He sentenced Stokes to 300 hours of community work with nine months' supervision with one special condition to attend and complete an appropriate programme determined by a probation officer.
Stokes must also pay Talleys back $10,000 at a rate of $40 per week.
