After intense lobbying by conservationists, hunters and sportsmen’s groups, Gov. Mark Dayton on Thursday used his line-item veto to cut off an attempt by legislators to override the Lessard-Sams Outdoor Heritage Council and fund a slate of habitat projects in metro parks.

The citizen council, which makes recommendations about how best to spend the animal habitat protection funds provided by Minnesota’s Legacy Amendment, backed about $9 million in grants for metro habitat protection. But the council did not favor spending $6.3 million on 15 regional parks projects.

That ignited a discussion about whether the metro area was getting its fair share of the funds and whether metro wildlife habitat is as deserving of the Legacy funds as habitat in outstate Minnesota. Jumping into the bitter debate, a bipartisan group of legislators decided to go against the Lessard council and pass a Legacy bill that included the money for the metro parks.

After the $496 million bill was passed, Dayton said he “heard from many organizations, representing thousands of our citizens,’’ who thought he would betray his promise to respect the recommendations of the council if he approved the metro parks habitat funding.

The governor also vetoed $3 million for aquatic invasive species control grants to tribal and local governments, also not recommended by the Lessard council.

The council, consisting largely of citizens, was created by the Legislature to help administer funds from the 2008 Clean Water, Land and Legacy Amendment, which raised the state’s sales tax to pay for outdoors and arts initiatives.

Dayton said his upholding of the council’s recommendations keeps his word to citizens “who care deeply about the Outdoor Heritage Fund of the Legacy Fund.”

But, he said, he would recommend that the Lessard council consider the metro parks requests in the next round of funding considerations, which will begin in June. Many of the projects involved prairie restoration efforts to provide habitat for waterfowl and other animals.

“I recognize this was a tough deal for the governor. I am happy that he chose to believe that our work was done well and thoughtfully,’’ said David Hartwell, council chairman.

The council has a fair, open process for choosing where to spend the money, Hartwell said, but “I think the message that we have to work even harder at being even more transparent isn’t going to be lost on us.”

Isis Stark, director of government relations for the Nature Conservancy in Minnesota, said: “We’re really happy that the governor has listened to the citizens on this issue.” Minnesotans want the best projects funded regardless of where they are in the state, Stark said.

Rep. Mike Freiberg, DFL-Golden Valley, a key sponsor of the House attempt to add funding for the metro parks projects, said he was surprised and disappointed by the veto. Projects to improve wildlife habitat in metro regional parks would have been very valuable, Freiberg said. “It wasn’t some fringe project. There was extensive bipartisan support for it in the House.”

The metro park districts are “somewhat disappointed if not very disappointed,” said Arne Stefferud, manager of regional parks and natural resources for the Metropolitan Council.

Anoka County Parks Director John VanDeLinde said metro park agencies will have to regroup “and try to do a better job of convincing the Lessard council that we are a major provider of fishing opportunities and we have over 30,000 acres of wildlife habitat, and that our mission very much parallels with the goals of the outdoor heritage council.”