ALBANY – Lawmakers here are mulling a tax increase on New York City businesses that could affect millions of consumers.

The state Senate last week rejected Governor Pataki’s plan to support transportation costs with a raft of motor vehicles fee increases, proposing instead to impose a 10% surcharge on taxes paid on business income from limited liability corporations, partnerships, and other unincorporated businesses within the service area of the Metropolitan Transportation Authority.

The new surcharge would help pay for the MTA’s $27.1 billion capital plan by broadening the category of businesses that are expected to pay into the giant network’s maintenance and support. The state currently imposes a 17% surcharge on top of the corporate income tax paid by corporations operating within the authority’s service area. The Senate, in which Republicans hold a majority, is now proposing to apply the tax to other businesses that are not organized as corporations.

According to the Senate proposal, which is said to be the subject of heated private negotiations at the state Capitol, unincorporated businesses including many accounting firms, law and medical practices, consulting firms, independent stores, contractors, gasoline stations, and others are being targeted for not paying into MTA’s costs.

These unincorporated businesses now pay taxes on their business income as part of the personal income taxes paid by owners of the business.

A budget analyst with the Empire Center for New York State Policy, E.J. McMahon, said the surcharge would hit businesses in New York City hardest. “This is a double whammy for New York because that’s the only city that has an unincorporated business tax,” Mr. McMahon said. “I think this will understandably annoy and upset a lot of businesses. By its nature, this hits the smallest, fastest-growing businesses and entrepreneurs, including people working in home offices. It would be the most significant business tax increase in recent memory.”

Sources familiar with the negotiations say lawmakers are looking for a way to tax these “pass-throughs” without hurting smaller mom-and-pop operations in the region. Those efforts are said to have proved extremely difficult so far.

An initial attempt at sparing fragile businesses involved adding the new surcharge onto taxes paid on business income over $45,000. That plan, outlined in the Senate’s budget proposal that was released last week, is now thought to be off the table.

The debate over the surcharge took on added significance this week as legislative leaders, under rare pressure to pass a budget by the April 1 deadline, sought to speed through negotiations. As of yesterday, members of the budget committee working on transportation remained at loggerheads on only three issues: the amount of money state residents should be asked to vote to borrow for transportation in a November referendum; the amount of federal money the state can expect to receive this year for transportation expenses, and the proposed surcharge on unincorporated businesses.

Also in the background of transportation negotiations is Mr. Pataki’s proposal to cover $14.7 billion of the estimated $17.2 billion cost of maintaining MTA’s core operations over the next five years. The governor is also proposing to spend $4 billion toward the $9.9 billion in capital expenses the MTA hopes to spend over the same period. The governor has proposed privatizing some MTA assets and selling others as a way of closing the gap. The Assembly and the Senate have agreed to ask voters for permission to borrow as much as $2.9 billion to close the gap.

Lawmakers may have devised the surcharge as a way of avoiding the fate of Gray Davis, the former governor of California who was recalled by voters in that state after imposing dramatic motor-vehicle fees in 2003. Governor Schwarzenegger, Mr. Davis’s successor, made repealing the fee increase one of his first official acts as governor. Mr. Pataki’s proposed fee hikes included a 75% increase in some motor-vehicle registration fees.

Politicians who back the surcharge, however, could still face the wrath of small businesses and business-advocacy groups that fear many firms will avoid the proposed fee by simply moving to another state or passing its costs along to clients.

“You’re talking about the most highly-mobile operations that have high-end professional employees that are already paying a very heavy income-tax premium for being in New York,” said the president of the Partnership for New York City, Kathryn Wylde. “The question is, what’s the tipping point for these companies that can pick up and move? And frankly, thanks to technology and telecom, they can operate from just about anywhere.”

A spokesman for state Senator Thomas Libous, a Republican of Binghamton and chairman of the Senate’s Committee on Transportation, said the proposal is under discussion but defended the surcharge as a way to defray costs by targeting businesses that currently benefit from the MTA without paying the surcharge for it that other businesses have for years. “This closes a loophole and finds funding for the MTA,” the spokesman, Bijoy Datta, said.

The proposed surcharge is one of two major debates over income-tax increases roiling budget negotiations this year. The governor’s budget calls for accelerating the December 31 termination date of a temporary income-tax surcharge imposed two years ago on high-income New Yorkers. The Assembly wants to make the tax permanent on those who earn more than $500,000 annually. The Senate is proposing to leave the sunset date where it is.

A spokesman for the governor, Todd Alhart, declined to say whether the governor will accept the Senate proposal if it makes it through budget negotiations. “It would be premature to comment before the conference committee meetings have concluded,” Mr. Alhart said.