A KiwiRail worker found them lying on the ground, where they were trying to regain their breath, the union said.
Union general secretary Wayne Butson told Radio New Zealand the workers would have inhaled fumes from machinery including compressors and generators, which had caused disorientation, nausea and giddiness.
Some of the contractors had not done tunnel gas training, and were not given the right gas masks, he said.
Mr Butson said KiwiRail's investigation lacked neutrality and the incident could have been avoided if KiwiRail had implemented recommendations from the union's earlier review of the Otira Tunnel.
The incident was not reported to the Ministry of Business, Innovation and Employment's safety investigators.
The ministry said it would make inquiries this week, and until those inquiries were made it would not be clear whether it should have been reported.
KiwiRail infrastructure and engineering general manager Rick van Barneveld told Radio New Zealand there had been a carbon monoxide incident which it investigated thoroughly, but there had been no nitrogen dioxide alarm.
The workers had been trained in tunnel procedures and, issued with the right gas masks and had gas monitor alarms.
Mr van Barneveld said the workers had returned to their vehicles when the alarm sounded, and were not overcome in the tunnel.
But he acknowledged they had not evacuated as quickly as they should have and were not given medical checks.
"The recovery procedure for a carbon monoxide incident, in an incident of this level, is in fact to have plenty of fresh air, something to eat and drink and to rest.
"All of that in fact happened, it was supervised and the men were in good spirits as they ended the day."
Mr van Barneveld said recommendations had been implemented and KiwiRail took any safety incident seriously.
He said the safety plan had not been specific enough on the day, and there was now a model evacuation plan for tunnel work.
Health checks would now be run immediately following an incident and the way workers underwent training had been reviewed.
"So we recognise that there were things that were not done as we think they should be. We learned from that and have those model plans in place."
A review of the Rimutaka Tunnel was underway and terms of reference for a more comprehensive look at the Kaimai Tunnel was in place.