SAN JOSE — BART officials had hoped to open the new Milpitas and Berryessa stations by the end of the year, as part of a long-awaited extension into Santa Clara County.

But the agency’s general manager revealed this week that BART is likely to miss that target, and trains probably won’t start taking passengers to those stations until sometime in 2020.

The culprit: More than 1,000 problems engineers have discovered since BART received the stations and tracks from the Santa Clara Valley Transportation Authority over the summer, delaying more intensive testing BART needs to do before its trains can carry passengers to the new stops.

While BART officials say a best-case scenario, in which the stations could still open before Jan. 1, is still possible, a postponement would represent the latest missed goal in BART’s Silicon Valley extension.

VTA, which is funding and building a $5.6 billion extension into downtown San Jose that BART will eventually operate, acknowledged last week that it has pushed back its estimate for when BART trains will reach planned stops at First and Santa Clara streets and at Diridon Station. Service there is now projected to start sometime in 2029 or 2030, rather than in 2026, as initially projected.

The stations in Milpitas and the Berryessa neighborhood are the first phase of BART’s extension south from Fremont’s Warm Springs stop. In an interview Monday, General Manager Robert Powers said BART engineers still need to do three months of “pre-revenue testing” at the two new stations, including exercises with first responders and scenarios meant to stress-test the new systems by simulating day-to-day problems.

“BART has assigned its very best engineers out in the field right now on the testing,” Powers said. “We are working just as hard as we can work, and I guarantee you I will open that system as quickly as we can open the system that is safe and reliable.”

But the testing has not yet started, and Powers declined to say when he thinks the stations will open.

“I won’t put a date on it,” he said.

Before pre-revenue testing can begin, Powers said, BART engineers need to fix “discrepancies” in the system, problems with components like the train control and power systems that the engineers have to work out. BART engineers had logged more than 1,200 discrepancies in total, of which about a quarter were resolved as of Sept. 16, according to a presentation the agency’s board received last week. More than half were considered “severe,” BART officials said.

VTA spokeswoman Bernice Alaniz said the number of problems that crews need to resolve before pre-revenue testing can start is much smaller — 48, according to VTA’s engineers. She said engineers plan to have those discrepancies resolved by Oct. 20.

If that happens, BART spokeswoman Alicia Trost said there is still the potential that BART could open the stations before the end of the year, if all goes well during a “compressed” testing period.

Alaniz described the number of discrepancies engineers have encountered as “typical” for a project of this magnitude.

Powers sounded a more optimistic tone about the extension into downtown San Jose, saying he believes BART and VTA are doing planning work that could “bring that date back in line” with earlier estimates.

“Any time there is a delay on something it’s a little frustrating, but we are doing what we can right now to set the project up to be successful in the future,” Powers said. “Maybe we can pull that date back a little bit.”