Options being considered include a taxi surcharge. On Wednesday, a key lawmaker said there were no deals yet.
Paterson wants lawmakers to agree on a plan to share the financial burden among drivers and transit riders.
Current proposals would result in across-the-board fare increases averaging 23 percent.
Subway and buses fares would rise from $2 to $2.50 on May 31. Long Island Rail Road and Metro-North fares, and bridge and tunnel tolls, would go up later.
The Senate started working on passing budget legislation Wednesday, but the action was halted when Senator Ruth Hassell-Thompson was feeling ill. She was diagnosed with what a Senate spokesman called "walking pneumonia."
The Assembly passed all nine budget bills Tuesday.
The budget legislation would increase state income tax rates on top earners, expand mandatory bottle deposits to water and further roll back tough Rockefeller-era drug sentencing laws.
Republican senators began offering amendments today, saying they were left out of budget talks.
The Democratic majority voted down Republican proposals to restore $7.4 million in library system funding and $14 million for nonpublic schools.
Finding a way to avoid the MTA Doomsday fare hikes and service cuts remains a sticking point. Some of the ideas being considered could hit commuters and even taxi riders.
Democratic State Senator Craig Johnson says, "Shame on you MTA, shame on you to bring us to the situation and not be willing to find some avenue of compromise."
Johnson represents Nassau county in Albany.
He claims suburbanites are fed up with MTA.
The idea of a business payroll tax that would have raised more than a billion dollars a year was nixed.
A business payroll tax was the main part of any deal preventing this summer's fare hike.
Governor Paterson said, "I haven't been happy about the developments over the last few weeks. But I certainly am chagrined!"
Now the governor's looking at starting over on an MTA bailout plan.
Lawmakers are considering raising the gasoline tax, higher auto registration fees, and perhaps a new 50 cent surcharge on every taxicab ride.
A surcharge taxi supporters find unfair.
"It's ridiculous to have the MTA want the taxi industry, a competitor, subsidize them," taxi industry lobbyist David Pollack said.
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