ST. PAUL — Gov. Mark Dayton used his line-item veto Thursday to strike two controversial provisions from the bill that uses state sales-tax money for grants to environmental and arts programs.

In deleting over $9 million from the $496 million Legacy Fund bill, Dayton acknowledged that he was forced to renege on a compromise he made with Senate Majority Leader Tom Bakk and House Speaker Paul Thissen in the final days of session. But he said that was necessary because of an earlier promise made during his gubernatorial run to supporters of the Lessard-Sams Outdoor Heritage Council, the state panel comprised mostly of citizens that reviews some applications for the Legacy Fund and makes grant recommendations.

Dayton excised $6.3 million for Twin Cities parks and $3 million to tribes and local governments to deal with aquatic invasive species.

While saying they were worthy programs, he noted neither was among the Lessard-Sams Council recommendations. Dayton, while running for office in 2010, had promised to support the panel’s recommendations.

“I attach great importance to keeping my word,” Dayton said in a letter to Thissen spelling out his line-item vetoes. “Unfortunately, in this instance, I have given contradictory assurances to legislators during the past few days and to thousands of Minnesotans during the past few years. I have decided I must honor my promise to those citizens.”

Grants from the Legacy Fund are fueled by a three-eighths-cent sales tax hike that voters approved in 2008. The money is split between programs covering arts and cultural heritage, outdoor heritage, environment and natural resources and parks and trails.

The Lessard-Sams Council is charged with recommending what programs should get the outdoor heritage portion of the fund. Dayton noted in his letter that disputes between state lawmakers and members of the council threatened to derail the entire Legacy Bill in the final days of session, and that his compromise with Bakk and Thissen was meant to save the bill from dying entirely.

“We might have written a very different bill if we thought we were facing a veto like this,” said Rep. Phyllis Kahn, the Minneapolis Democrat who drafted the two struck provisions. She said she included the money for research into preventing aquatic invasive species — a problem facing many of Minnesota’s lakes — because she feels the Lessard-Sams Council has overly stringent standards.

“I guess we try again next year,” Kahn said. Thissen and Bakk did not immediately respond to Dayton’s vetoes.

Dayton wrote that he hoped recreation groups would accept the compromise. But, he went on, in the last few days many organizations told him that leaving those two provisions in the bill would have betrayed numerous promises he had made. Among the groups requesting Dayton’s veto were the Nature Conservancy and two dozen other habitat and sportsmen’s groups.

Dayton warned of “acrimony and distrust” between legislators and those groups, and said the relationship must be repaired, “Otherwise, I have serious doubts that a Legacy Bill can be enacted in future legislative sessions.”

The bill also contains a provision that directs the city of St. Paul to issue a beer and wine license to the rathskeller-style cafeteria in the basement of the state Capitol.