But when pressed for an explanation by coach Stacey Jones, the NRL stood by the captain's challenge process that prevented the Kiwis from kicking for a game-winning penalty goal.
His side down a point in the final minute on Saturday night, Kiwis halfback Shaun Johnson lined up for a field goal from point-blank range but had his shot charged down by Tonga's Jason Taumalolo.
Kiwis skipper James Fisher-Harris mounted a captain's challenge when the play broke down, believing Taumalolo had illegally contacted Johnson's legs as he kicked.
The challenge was unsuccessful, denying the Kiwis a chance to kick for a penalty goal and booking Tonga a date with Australia in Sunday's Pacific Cup final.
On-field referee Todd Smith had missed Tonga second-rower Eliesa Katoa not being square at marker when he ran towards Johnson.
When Jones called referees boss Jared Maxwell seeking an explanation, the coach was told the Kiwis should have been awarded an immediate six-again given Katoa had been offside.
In that case, Johnson may not have kicked for field goal on the last tackle, and the Kiwis would have had another set to attack the Tongan line in pursuit of points.
A draw would have been enough to send the Kiwis to the tournament showpiece at CommBank Stadium.
"That was disappointing because we didn't get six again and what happened there was clearly an infringement," Jones said.
"It's frustrating for all the effort goes into a big game like that.
"But people get things wrong."
AAP understands the NRL's view is referee Smith was at fault for the miss, but the bunker was not to blame.
When they spoke to Smith in mounting their on-field challenge, Johnson and Fisher-Harris urged the bunker to consider Katoa's movements.
But ruck and marker infringements are not able to be disputed in a captain's challenge, so bunker official Wyatt Raymond could not rule on Katoa's movement.
"Marker and 10m offences are not challengeable. In this incident, the play continued (past the non-call on Katoa) and the captain's challenge was for an entirely different incident," NRL head of football Graham Annesley told AAP.
Jones did not blame the refereeing decision for the loss that consigns the Kiwis to a clash with Papua New Guinea to avoid relegation to the second-tier Pacific Bowl next year.
The Kiwis instead rued falling behind 24-0 late in the first half before drawing level in the final 15 minutes.
"They said they couldn't go back and check the markers. I'm not too sure, there are so many grey areas in challenging and whatnot," Jones said.
"At the end of the day we shouldn't have been in that position."
