Henderson, who was set to contest the cycling road race in Delhi, announced yesterday he was pulling out of the Games, saying he could no longer think only of himself.
"It's not just about me. I've got a family now and they've got to be part of anything I do," he said.
"I've got four Commonwealth Games medals and I've got the world champs coming up next week and I start training again in January for the next pro season. In the end, all the cons outweighed the pros. It was an easy decision to make."
The former Dunedin rider cited worries over terrorism, dengue fever and the accommodation hassles as all contributing to the decision not to go.
Photographs of the poor conditions of the Games village were the final straw which led to him pulling out.
Gail and Bob Henderson, who have been to every Commonwealth Games and Olympics their son has competed in, had earlier decided against heading to Delhi because of worries over security and accommodation.
Last night, New Zealand Olympic Committee president Mike Stanley said the country was preparing to be at the Games unless issues remained that could not be resolved.
Mr Stanley said planning for the first of the New Zealand athletes to check in from next Tuesday - three days later than the original schedule - was continuing.
Henderson (34) is coming off a heavy road season, and has just completed a tough Tour of Britain, where he finished third after winning the second stage.
He said with a busy season of cycling, he had tried not to think too much about whether he would head to Delhi.
"I just tried to concentrate on the bike and the racing, but I suppose it was at the back of my mind. The first time we had time to sit down and think about it was when we started coming back here."
Henderson, wife Katie Mactier, and daughter Charlie (13 months) have returned to their Melbourne base from the United Kingdom.
Henderson is now preparing for the road cycling world championships in the city.
He said it was not a long discussion over whether to pull out of the Games.
"I'm very comfortable with the decision. It's been playing in the back of my mind and now that the decision has been made I can move on. It was not a decision I took lightly."
Asked if he was showing disloyalty to his country by not competing, Henderson said he had represented New Zealand at many events and would be back to win in 2012 at the London Olympics.
Four Sky Pro cycling team-mates also pulled out yesterday but when Henderson spoke to the Otago Daily Times he was not aware of that.
He said there was no team order for riders to pull out and team bosses recognised the Games were about national representation and any decision was up to individual riders.
He was now putting all his energy into the 267km road race at the world championships on October 3.
Gail Henderson said she and her husband backed their son's decision.
"We had no intention of going to this one. I guess we've been proved right. I think he [Greg] has made the right choice," she said.
