Fiji rugby announced on Friday the team would front the All Blacks at Forsyth Barr stadium wearing shirts with the message "Vaccinate Fiji" emblazoned on the front.
"We are humbled and delighted that our national airline has given up their prime 'front of jersey' space in this test series for the greater good, replacing their own brand with the message: 'Vaccinate Fiji'," O'Connor said.
"Our Flying Fijians will proudly carry on this message in the two games to encourage our people to get fully vaccinated to win the fight against Covid-19."
After opposition from players, however, the Fijian team that scored three tries and seriously tested the All Blacks before fading in the 57-23 defeat did so in jerseys that did not display the vaccination message.
Asked about the situation post-match, Cotter attempted to explain what had transpired.
"It's a really complex answer. We haven't really got the full answer other than it was sprung on the players quite late in the piece with not a lot of exchange and consultation," Cotter said.
"As you can imagine it's a delicate subject for some so it was probably better to have a clean jersey at this stage and spend some time on how we best want to communicate on this matter and how comfortable the players and everyone are in communicating with regard to that.
"The team showed solidarity and strength in what they did with the decision to postpone a real communication on it, and the way they played will inspire people in Fiji to play rugby. These guys were role models."
Daily cases of Covid-19 in Fiji continue to rise, with more than 5000 active in a population of less that 1 million. It included a rise of 860 cases on Friday and three deaths - one of which was a 15-year-old.
Cotter, a former Crusaders assistant and Scotland head coach, suggested more discussions would take place on the issue of the vaccination message.
"It's complex, we need to work it out because it's not just sport we're talking about now so we'll take time and try and communicate better in future.
"Covid for everybody is hard. It's changed the way everybody lives all over the world. These guys that are based in Europe are living with it every day and Fiji is now getting struck with it and it's gone through a lot of countries.
"It's a sensitive issue and everybody is aware of what's going on and these guys here they just want to play rugby and play well - to show they are representing their country and people by putting in brave displays on the paddock."
After Fiji's impressive display in their first match against the All Blacks for 10 years, Cotter hoped governing body World Rugby would sit up and take notice to provide more fixtures against the world's best teams.
The last members of the Fiji squad emerged from quarantine on Wednesday and they only held two full trainings together before challenging the All Blacks. Three Fijian players remain stuck in Australia, unable to travel to New Zealand to join the squad.
"If you can get those games more often you get to measure yourself against the best and you improve. They've shown enough in this game to be offered more opportunities to play those teams - I hope so," Cotter said.
"It's a great challenge that can develop the Fijian talent.
"They're amazing, explosive athletes and it's a joy to watch them play. When you see them throwing themselves around the paddock... to see them more often against good teams it'd be great.
"We're not satisfied with it, we want to get better, but it was a good start."
