Texas Gov. Rick Perry, under questioning from voters in recent days, has switched positions on a 2007 executive order he issued mandating the vaccination of all young girls before they enter sixth grade to ward off cervical cancer.

Mr. Perry’s order that Texas school girls receive the vaccine, Gardasil, made by Merck & Co., was overturned by the state legislature and never got off the ground. But it still has roiled conservatives and Christian groups for years.

After long defending the decision, Mr. Perry has apologized repeatedly for the order since launching his bid for the Republican presidential nomination. As recently as his 2010 gubernatorial re-election bid, Mr. Perry touted the vaccine’s medical efficacy and the lives of young women it saved.

Critics, especially on the right, contended it seemed out of line with Texas’ abstinence-only sex-education policies—the vaccine targets a virus spread by sexual contact—and parents’ rights in that area.

During interviews and conversations with voters this week, Mr. Perry said he was sorry for his Gardasil decision. “I didn’t do my research well enough to understand that we needed to have a substantial conversation with our citizenry,” he said at a voter gathering in New Hampshire. He told a TV news reporter in Iowa, “We backed up, took a look at what we did. I understand I work for the people. It’s not the other way around.”

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The Gardasil controversy has resurfaced as Mr. Perry is positioning himself not only as an antiregulation job creator, but also as a religious conservative on social issues. The latter stance puts him in direct competition with Rep. Michele Bachmann, a Minnesota Republican who has strong support among such groups.

His switch seems to have calmed some of his harshest critics, including the Family Research Council, a conservative advocacy group that focuses on social issues. It fought the 2007 mandate saying it infringed on parental rights. This week, the group’s president, Tony Perkins, applauded the change, saying Mr. Perry’s original order, which he called “a bad decision,” was based on Mr. Perry’s “concern with protecting human life.” Added Mr. Perkins in an interview: “I’m satisfied with what Mr. Perry has stated now.”

Republican Sen. Kay Bailey Hutchison of Texas, who ran against Mr. Perry in the 2010 gubernatorial primary, raised the Gardasil issue in a TV ad. The ad suggested the decision was driven by Mike Toomey, a former top Perry aide who is also a lobbyist for Merck, which pushed for Gardasil programs in at least 20 states.

Perry spokesman Mark Miner said, “There was no influence whatsoever” from Mr. Toomey, who is now running one of the largest outside groups raising funds for the Perry presidential bid. Mr. Toomey didn’t respond to requests for comment.

Merck said in a written statement its focus was saving girls and women from cervical cancer, and it cited studies performed since the vaccine was approved in 2006 that demonstrate its efficacy.

The Centers for Disease Control and Prevention recommended a series of three treatments, which the company says cost about $130 each. To work effectively, the vaccine should be administered before a girl is infected. Because numerous studies show that girls are becoming sexually active at younger ages, health officials approved the vaccine for preteen girls.

In 2007, members of the Texas state legislature strongly opposed the mandate. In addition to questions about the state’s sexual-abstinence policy, they also complained about the cost to Medicaid. Mr. Perry signed an executive order to get around the legislators’ objections. Though it included an opt-out provision, the policy inflamed conservative groups around the country as well as Texas lawmakers.

At a news conference that May, after state lawmakers voted to block the vaccination order, Mr. Perry criticized his opponents. “I challenge legislators to look these women in the eyes and tell them: ‘We could have prevented this disease for your daughters and granddaughters, but we just didn’t have the gumption to address all the misguided and misleading political rhetoric,’ ” he said.

In 2010, when Mr. Perry was asked in a gubernatorial primary debate if he had made a mistake supporting Gardasil, he replied, “No, sir,” adding, “I stand proudly by my pro-life position.”