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Gov. Frank Murkowski said Tuesday afternoon in a written statement that the lawsuit will clarify who retains the rights to Alaska waters and tidelands in areas such as Cook Inlet and Bristol Bay.

The state claims that the Interior and Agriculture departments haven't followed U.S. Supreme Court criteria for establishing water rights. The complaint cites the Nushagak River in Bristol Bay, the Egegik River on the Alaska Peninsula and marine lands and tidelands at Tuxedni Bay on Cook Inlet.

Loss of control in such areas hinders the state's ability to develop natural resources under and adjacent to the water bodies, the state's Fish and Game Department commissioner said Tuesday. It also allows the federal government to dictate user groups' access to fish and wildlife.

In 1999, the federal government issued subsistence regulations on navigable waters running through or adjacent to federal land. In the past, sportsmen complained about federal control over these areas, but many Native subsistence users welcomed federal management.

"This case does not challenge title VIII subsistence provisions or the Katie John decision," Murkowski said in a written statement Tuesday. "It simply represents my commitment to vigorously defend Alaskans against an over-reaching federal government."

The state had five years to appeal the 1999 regulations. The clock runs out on Friday, according Wayne Regelin, acting commissioner for the Department of Fish and Game.

"Negotiations and discussions have failed to achieve any results," Regelin said.

It is unclear if the lawsuit would have a major effect in Southeast Alaska, where much land and some interior waters are under federal jurisdiction already. But Regelin said he knew it was a big concern in Interior Alaska, where federal jurisdiction could affect resource development and subsistence management.

An underlying problem that has been festering for more than a decade is the conflict between state and federal definitions of use of subsistence resources. Federal subsistence rules say subsistence rights are granted to rural residents, with a priority for Native users. That conflicts with the Alaska Constitution, which makes subsistence resources available to all Alaskans. The state has more restrictive criteria for establishing subsistence hunts and fisheries.

The disputed land has been under federal jurisdiction since statehood, said John Littlefield, an Alaska Native and chairman of the Southeast Regional Subsistence Board. "They should not be suing over anything the federal government owned at the time of statehood," he said.

"I have reached out to leadership of the Alaska Native community to advise them of the state's action and the reasons behind it," Murkowski said.

• Timothy Inklebarger can be reached at timothy.inklebarger@juneauempire.com. Elizabeth Bluemink can be reached at elizabeth.bluemink@juneauempire.com.