In an effort to secure federal funds by cutting $1.3 billion from a BART extension through downtown San Jose, planners are considering eliminating two of four stations — and neighborhoods that had been counting on those stations are up in arms.

On the chopping block are two planned stops, one at 28th Street behind Five Wounds Church near Highway 101 in San Jose, and one across from Santa Clara University. A proposed maintenance yard at Newhall Street would also be cut and that facility used just to turn trains around.

Stations would be built under Santa Clara Street near Market and at Diridon Station across from the Sharks arena, under the plan being considered by the Valley Transportation Authority. Another proposal would build a third station near 23rd Street instead of 28th.

“This doesn’t make any sense,” said Joan Rivas-Crosby, chair of the Five Wounds Trail group, which believes BART is essential to reviving the Alum Rock neighborhood around 28th Street. “BART is very popular with us but we now feel totally left out in the cold.”

Santa Clara Mayor Jamie Matthews said he understands the financial challenges, “but this is nonsense.”

The money hurdles are enormous. A four-station, six-mile route would cost $4.7 billion, compared with $3.4 billion with two stations.

The VTA has as much as $1.4 billion in sales tax approved by voters 14 years ago and is banking on at least $1.1 billion in aid from the Federal Transit Administration. A new sales tax will almost certainly be on the ballot in 2016 and if approved could make up much of the shortfall if the scaled-back plan is adopted.

Getting federal aid might not be as easy as with the 10-mile extension from Fremont to the Berryessa area of San Jose east of 101. The VTA secured $900,000 from Washington for the $2.3 billion line. That phase is under construction and could open in three years.

But requests for federal funds have soared, with transit agencies nationwide competing for assistance.

The original plan to extend BART through downtown San Jose with four stations has a moderate to low ranking with the Federal Transit Administration. But with only two depots, the ranking improves to the moderate to high level.

“We are looking at the best project that we can fund and build and that FTA will support,” VTA spokeswoman Bernice Alaniz said. “It’s not just up to us.”

Federal officials might set new, more stringent requirements for land-use plans, and they want local agencies to have at least 50 percent of the needed funding. The VTA wants to approve environmental studies by the end of the year so it can go to the FTA by summer, before more stringent requirements might be in place.

The Santa Clara station could be built later, but that could be many years in the future if it doesn’t make the current cut. But the 28th Street stop is in danger of not happening.

San Jose Councilman and VTA chair Ash Kalra holds out hope that the eastside station along Alum Rock at 28th can be saved.

“I am committed to that,” he said, “but it’s going to take a lot of creative work. It’s not going to be easy.”

Added Carl Guardino, CEO of the Silicon Valley Leadership Group, “We have to be competitive for federal funds, but I hope and believe we can get cost-effective numbers with three stations.”

Money would also be saved by running BART tracks over instead of under Highway 101 and starting the tunnel segment a quarter of a mile later, west of 101. But the 2,500-space, four- to six-story BART parking garage at 28th would be lost, and there are no plans for parking at 23rd Street if a station is built there.

Eliminating the 28th Street station could also hurt the development of the Five Wounds Urban Village, which has been more than a decade in the planning.

If the decision is to eliminate the 28th Street stop, it could affect the 2016 sales-tax campaign, warned Rivas-Crosby, who said her group might fight a new tax if the VTA station cuts occur.

“Our stance is non-negotiable,” she said. “The station has to be there.”

Contact Gary Richards at 408-920-5335.