New Zealand Football (NZF) chief executive Andy Martin declared the eligibility confusion that saw the body's under-23 side dumped from Oceania's Olympic football tournament was "hugely embarrassing".
But Martin insisted NZF is convinced it did the right thing in playing South Africa-born defender Deklan Wynne at the tournament in Papua New Guinea, although it is yet to lodge an appeal as lawyers research the case.
"We wouldn't have fielded him in any game if we didn't believe it was right," the chief executive said.
Either way, Martin was disappointed with how the incident had left a black mark on NZF's reputation.
"This is hugely embarrassing for New Zealand Football and for football," he said at a media conference on Tuesday.
"I think we have done a lot of great things in the last 12 months in terms of getting football on the map in this country. The success of the Under-20 World Cup has really given us great momentum.
"Right now I just want to apologise for that embarrassment."
New Zealand were set to play Fiji in the Oceania Olympic qualifying final on Sunday but did not take part after a protest from Vanuatu was upheld regarding Wynne's eligibility.
Vanuatu, who had lost Friday's semi-final 2-0 to New Zealand, then succumbed in the final after a penalty shoot-out.
Martin explained how NZF "continually sought clarity" on the eligibility rules before the event, which was also part of the quadrennial Pacific Games, while he also outlined how the team had been made aware of Vanuatu's protest.
The issue appears to be which rules apply - FIFA's Olympic regulations or those of the Pacific Games.
New Zealand's team manager first heard of the protest thanks to "a typed unheaded paper notice" after the semi-final as he boarded the bus to return to the team's hotel.
Correspondence continued on Saturday but NZF was told on Sunday that a disciplinary hearing had already been held to rule on the issue.
"We do not know who sat on that committee," Martin said.
Speaking on Monday, the young man at the centre of the saga reiterated his commitment to play for his adopted country rather than South Africa.
Wynne, 20, has already played for New Zealand's senior side three times.
"I'm just really disappointed. But I have the backing of the boys and NZF has got my best interests at heart so I just have trust in them," he said.
