Transit officials sent a mixed message yesterday, voting to authorize $50 million to cover discount fares for the holidays even as they are asking riders to approve a $2.9 billion transportation bond on November 8.

Prior to the 12-2 vote by the board of the Metropolitan Transportation Authority yesterday, board members said they were concerned that the giveback would weaken their case with voters.

“There is another thought out there, which is the MTA is awash in money,” a non-voting board member, Andrew Albert, said of riders’ perception of the financial state of the MTA. “I’m afraid that the unfortunate timing of this could be a drag on the passage of the bond issue, which we all agree is of the utmost importance.”

The plan approved yesterday includes half-price weekend bus and subway fares between Thanksgiving and New Year’s at a cost of $50 million, or 5% of the projected $1 billion surplus.

The chairman of the MTA, Peter Kalikow, said a decision to go ahead with the discount program had to be made yesterday in order to give the transit authority enough time to put the program in place before Thanksgiving.

“I share your view of the precarious position that the bond act is in,” Mr. Kalikow said to Mr. Albert, adding that the discounts would not stave off a fare increase set for 2007.

Advocates for the bond act shared similar worries.

“It’s a very serious concern,” a spokesman for the Regional Plan Association, Jeremy Soffin, said via email. “All we can do is explain the reality of the situation: that this is a one-time surplus and that the MTA’s long-term needs far exceed its current funding. Surplus or no surplus, without the Bond Act we’ll have no system expansion and will likely face service cuts or fare hikes.”

Most of the money from the bond would fund expansion projects, such as plans to build a Second Avenue subway and efforts to bring the Long Island Rail Road to Grand Central Terminal. About $450 million would go toward basic maintenance of the system, costs listed in the MTA’s budget that were not approved by the state.

Some board members and critics of the holiday discounts have said the surplus should be focused on filling budget gaps and long-term needs. An advocate for disabled riders, Michael Harris, said the authority could use the $50 million to buy 20 new elevators at $2.2 million each or at least fix the 25 elevators that are out of service.

The larger questions of how the bulk of the MTA’s surplus will be allocated will not be addressed until the board meets next month.

The surplus is estimated to be nearly $1.1 billion, of which $700 million comes from a one-time tax windfall related to the real estate boom. The authority has proposed using $450 million of the surplus to pay off unfunded pension obligations, a decision that has been roundly lauded by transit and budget experts, as it will save the authority $40 million annually. Mr. Kalikow said the decision by past MTA boards not to fund the pensions was a “disgrace.”

Two board members representing suburban commuters, Mitchell Pally of Suffolk County and Andrew Saul of Westchester County, voted against the fare discount. Mr. Pally criticized a part of the plan that will offer a free 10-trip pass to suburban commuters who purchase December monthly passes, saying the free pass can be used only during off-peak hours. Those who buy weekly and monthly MetroCards do not have similar restrictions.

“I believe the plan as envisioned is unfair to suburban commuters and gives significantly more benefit to city riders than suburban commuters,” Mr. Pally said.

Governor Pataki complicated matters Wednesday by proposing to spend $250 million of the surplus on transit projects for Lower Manhattan, including a proposed rail link between Lower Manhattan and JFK Airport. Mr. Pataki has long favored the project, but it has little priority at the MTA, setting up a potential conflict between the governor and Mr. Kalikow, who is a campaign contributor and appointee of Mr. Pataki.

“There are many, many, many claims on the money the MTA has, and it’s not an easy job to decide where the pieces should be distributed,” Mr. Kalikow said.