JACKSON (AP) — It now appears unlikely that Mississippi lawmakers will be able to increase the cigarette tax this special session to fill a $90 million hole in the Medicaid budget.

Lt. Gov. Phil Bryant ruled Thursday that the cigarette tax is outside the agenda that Gov. Haley Barbour set.

A governor controls the subjects lawmakers may consider in special session. But some Democrats have argued that the governor can’t limit the way those subjects are handled. They say, for example, that Barbour can tell lawmakers to fix the Medicaid budget but can’t tell them how to do it.

Bryant ruled that Barbour’s agenda specifically called for restructuring hospital taxes to help pay for Medicaid, a health program for the needy.

‘‘I believe this is a difficult decision but it is an important one,’’ Bryant said.

Barbour and Bryant are Republicans. Bryant says his ruling was not political but was based on his interpretation of the state constitution.

The Mississippi Hospital Association endorsed Barbour’s plan weeks ago, but several hospital administrators have said since then that they don’t want their taxes to increase.

Health advocates say increasing the cigarette tax would generate millions of dollars.

Mississippi’s cigarette excise tax is 18 cents a pack. That’s the third lowest in the nation, behind only Missouri and South Carolina.

Several Senate Democrats, including David Jordan of Greenwood, argued that increasing the cigarette tax would help resolve Medicaid’s budget problems and would ease the minds of patients and providers who rely on the program.

‘‘We ought to not be down here playing Russian roulette with people’s lives,’’ Jordan said Thursday.

The special session started in late May, but the House and Senate got stuck in disagreements about Medicaid. Thursday was lawmakers’ first day back after a three-week break.

There was little action on the House floor Thursday as members of that chamber waited to see whether Bryant would let the Senate consider a cigarette tax bill.

The Democratic leadership of the House has been pushing a tobacco tax increase to help pay for Medicaid, but they’ve been unable to get enough votes so far. Even if the House can pass a tobacco tax bill, Bryant’s ruling means the bill would die in the Senate.

The chief executive officers of two hospitals told a House committee Thursday they’re worried that Medicaid’s problems could hurt their facilities.

Ray Humphreys of Delta Regional Medical Center in Greenville said his hospital might have to lay off employees if he’s forced to cut his budget.

Gary Marchand of Memorial Hospital at Gulfport said that if Memorial’s expenses increase, the hospital might pass on some costs to private insurers.

The new state budget year begins Tuesday. It’s not unusual for Medicaid to go the first six months of a budget year with a shortage of money, but the program is usually able to pay its expenses. Barbour says he’s tired of the budget problems and he wants a solution soon.