The MBTA has promised a lot of major upgrades. But can it afford them all?

A revamped bus system with new routes and more bus-only lanes. A radical expansion of commuter rail service, with trains every 15 minutes on some lines. And, following an outside report documenting lax safety practices at the MBTA, a pledge to improve standards across the system.

These are among the major initiatives the Massachusetts Bay Transportation Authority has promised in recent months, buoyed by new internal offices and staff to oversee the projects.

But with budget season now underway, it’s not clear the authority can fully afford the estimated $160 million cost just to get the projects and other new initiatives off the ground.

At a board meeting on Monday, chief administrative officer David Panagore said the MBTA is facing a $93 million budget deficit for the fiscal year that starts July 1, according to a preliminary estimate. Cutting some proposed funding for the bus and commuter rail “transformation offices" and new safety programs could help balance the budget, which may top $2.35 billion, he said.

“In terms of our budget, we cannot afford all $160 million,” he said.

Panagore did not suggest eliminating any of the new programs, which also include support for new fare-collection equipment, increased service on peak-hour bus routes, and a new “flex force” to complete infrastructure work quickly. Instead, the MBTA could reduce each program’s price tag by a quarter, reducing the projected deficit by about $40 million.

But governing board members said they wanted more detail about how the cuts would affect the programs before voting on the budget, which must be finalized by mid-April.

Vice chair Monica Tibbits-Nutt said the potential budget reductions could hurt the MBTA’s credibility.

“This does not seem consistent with what we told the public," Tibbits-Nutt said. “If we are not going to spend the amount of money needed to achieve these, then we need to be very, very clear with the public about what is not going to happen.”

The MBTA is facing a deficit even though it expects to receive an additional $135 million in state funding this year from increased sales tax collections and a proposal by Governor Charlie Baker to boost government fees on Uber and Lyft trips.

Lawmakers in the House of Representatives are also expected to unveil legislation soon that could increase MBTA funding, possibly by raising the gas tax or bolstering other revenue sources. But Panagore said it is premature to factor any of that potential money into the budget.

“I operate on the money that is presented . . . The rest of it is speculative,” he said.

Another board member, Brian Lang, wondered whether the budget gap could be closed by reducing other costs, such as the MBTA’s contribution to its pension system. But he acknowledged that such a daunting issue was unlikely to be settled this budget cycle.

Panagore said that boards like the MBTA’s, created nearly five years ago to help get costs under control, often struggle to find savings after the first few years.

“Your first several years, you get rid of the low-hanging fruit,” said Panagore, who previously worked on municipal government turnarounds in Springfield and Chelsea. “You’re now in the fourth- fifth-year zone. It is much harder to find.”

Technically, the operating budget for the next fiscal year is nearly balanced. But the MBTA prefers to transfer $90 million from operating funds each year to its capital budget to pay for construction projects to repair and modernize the system. That transfer would account for nearly all of next year’s gap.

While the annual operating budget will pay for staff and other office resources to oversee the various new projects, the capital budget funds most of the actual infrastructure work — adding vehicles, replacing tracks and signals, and expanding the Green Line to Somerville and Medford. The bus, commuter rail, and fare-system projects would require significant capital funding, but the costs discussed Monday referred primarily to staffing to oversee the work.

The board also received an update on another long-discussed initiative, a discount for low-income riders. Officials said it would take at least a year to implement such a program.

Among the challenges: Who would administer the program? Who would qualify? And how would it be funded, given that the total costs in added operations and lost fares could exceed $50 million a year, adding to the budget pressures?

Secretary of Transportation Stephanie Pollack suggested that foundations or municipalities should help fund a low-income fare.