New Zealand coach Stacey Jones has been told the referees made an error during their narrow defeat to Tonga. (Andrew Cornaga/AAP PHOTOS)

New Zealand have been told the referees made an error in the final moments of their 25-24 defeat to Tonga, which could have deprived the Kiwis of the chance to secure their place in the Pacific Cup final.

But when asked for an explanation by coach Stacey Jones, the NRL went ahead with the captain’s challenge process which prevented the Kiwis from scoring a winning penalty.

With his team down a point in the final minute on Saturday night, Kiwi halfback Shaun Johnson lined up for a point-blank field goal, but his shot was saved by Tonga’s Jason Taumalolo.

Kiwi skipper James Fisher-Harris issued a captain’s challenge when the play broke down, believing Taumalolo had illegally touched Johnson’s legs as he kicked.

The challenge failed, denying the Kiwis a chance to score a penalty and booking Tonga a date with Australia in Sunday’s Pacific Cup final.

On-field referee Todd Smith had missed Tonga’s second rower, Eliesa Katoa, who was not right side up at the marker when he ran towards Johnson.

When Jones called referee boss Jared Maxwell to demand an explanation, the coach was informed the Kiwis should have been awarded an immediate six given Katoa was offside.

In that case, Johnson might not have made the field goal on the final tackle, and the Kiwis would have had another set to attack the Tongan line in search of points.

A draw would have been enough to send the Kiwis to the tournament showpiece at CommBank Stadium.

“It was disappointing because we haven’t scored six yet and what happened there was clearly an infraction,” Jones said.

“It’s frustrating because all the effort is necessary for a big match like this.

“But people are wrong.”

AAP understands the NRL’s view is that referee Smith was responsible for the miss, but the bunker was not to blame.

When chatting with Smith about preparing for their on-field challenge, Johnson and Fisher-Harris urged the bunker to take Katoa’s moves into account.

But ruck and marker infractions cannot be challenged in a captain’s challenge, so bunker manager Wyatt Raymond couldn’t comment on Katoa’s move.

“The marker and 10 meter infractions are not questionable. In this incident, play continued (beyond the non-call on Katoa) and the captain’s challenge was in relation to a completely different incident,” NRL head of football Graham Annesley told AAP.

Jones did not blame the refereeing decision for the defeat which forces the Kiwis into a clash with Papua New Guinea to avoid relegation to next year’s second-tier Pacific Bowl.

The Kiwis fell behind 24-0 late in the first half before coming back to level terms 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 gray areas when it comes to challenges and so on,” Jones said.

“At the end of the day, we shouldn’t have found ourselves in this position.”