SAN YSIDRO – A lack of funds could complicate the last two phases of the expansion project at the San Ysidro border crossing, federal authorities said.

"Those decisions depend on the Congress. Right now we're waiting for the resources to begin to plan Phases Two and Three," said Damon Yee, the project manager of the expansion for the General Services Administration (GSA).

The two phases at risk are the remodeling and expansion of the building that houses the pedestrian crossing and the realignment of Interstate 5 to connect to the area known as El Chaparral, where the southbound port to Mexico will be located.

The entire project was to be completed by 2016, but that date is in doubt because Congress has not allocated the funds needed for Phases 2 and 3.

That's not all that could be affected. Expansion plans for Otay Mesa and Calexico ports could also be delayed.

"At this point we don't have any idea what is going to happen," Yee said in an interview on Friday.

He said that the priority is to expedite crossings at the San Ysidro port of entry and once that expansion is finished in 2014, the focus will shift to other sites.

He said a delay in funding does not mean that the expansion project will not be completed, rather that it could take much longer than planned.

The expansion of the San Ysidro port -- where about 50,000 vehicles and 25,000 pedestrians cross daily into the United States -- is to cost $577 million.

Currently, the project is in phase 1C, in which the structure above the U.S.-bound lanes will be demolished.

That's why U.S. Customs and Border Protection (CBP) officials announced that some lanes will be temporarily closed starting in two weeks.

However, additional inspection booths are being added so two vehicles can be inspected per lane at a time. The goal is for 24 gates to be operational, despite the lane closures.

"The idea is to not affect wait times in any way," said Oscar Preciado, CBP's project director.

Preciado said his agency is in communication with authorities in Tijuana so they can put up signage to indicate which lanes are open.

Lanes will be temporarily closed from the beginning of September through the last week of November in periods that are not to exceed 30 hours.

In July, when the CBP closed some lanes temporarily, the wait times increased by as much as an hour, frustrating many drivers, particularly during the morning commute.

"The wait has been extremely long, much more than before," said Juan Miguel Reynoso at the time, noting he crossed every day to go to work in San Diego.

alexandra.mendoza@sandiegored.com