New Hampshire thus will become the fourth state to adopt civil unions and the first to do so without first having a court fight over denying gays the right to marry.
"I believe it is a matter of conscience, fairness and preventing discrimination," Lynch said in an interview.
Although Lynch had said previously he supports expanding health benefits to same-sex partners of state workers, he had declined to take a public position on civil unions. He came under fire from both sides for not weighing in — especially after the surprise delay last week of the Senate vote on the House-passed bill.
Some legislators had worried the Democratic governor might part company on the bill with Democrats who control the House and Senate for the first time in more than a century.
He said he announced his position on the bill after extensive discussions with lawmakers, including most of the 24 state senators.
"I wanted to see that healthy debate happen in the Statehouse," he said.
The Senate votes on the bill next week, and Lynch said he is confident it will pass. It would authorize civil unions beginning next year.
New Hampshire will hold the earliest presidential primary next year, and candidates have been visiting the state regularly. Lynch said he doubts the enactment of civil unions would have any effect on the primary campaign.
Asked about political fallout in state races, he said, "I don't think that's a relevant question."
State Republican Chairman Fergus Cullen disagreed.
"You're kidding," he said when first told of Lynch's decision.
"The Democrats are going too far, too fast and Governor Lynch is going along with them," he said. "These are not the actions of a moderate governor."
In the interview, Lynch noted his support for same-sex benefits when he was a trustee in the state university system. But he has said he opposes gay marriage.
Asked why he opposes gay marriage but supports civil unions, Lynch said, "I still think marriage is between a man and a woman, but this prevents discrimination."
Neighboring Massachusetts, the only state that allows gays to marry, did so after a court decision mandating it. Vermont and New Jersey also responded to court orders when they legalized civil unions.
Connecticut became the first state to legislate civil unions without court intervention two years ago. A lawsuit challenging Connecticut's marriage law was pending, but legislators said they were not influenced by it.
The House passed the bill nearly 2-1 on April 4.