"The most recent analysis" of the agency's $7.3-billion East Side Access plan put the expected opening date in 2019 -- a year later than the last review, Lhota told a Long Island Association meeting of business, community and elected leaders.
"It's my expectation -- 2019," he said.
While the agency is still aiming to finish the so-called megaproject by 2018, various complications could delay it until the next year, Lhota said in an interview after the meeting.
"If everything bad happens, it might push it out a year," he said. "I'm doing everything I can to keep it at 2018."
The East Side Access plan, which Lhota called the "largest public works project currently going on in the United States," will link the LIRR to Grand Central through newly bored tunnels in Manhattan and Queens.
Lhota said the project will save about 160,000 LIRR riders at least 40 minutes a day on their commutes. It also will raise property values in Nassau and Suffolk counties by making Long Island more attractive to people who work on Manhattan's East Side, he said.
Late last year, MTA officials said they were still working to hit the previous target completion date of 2016, and vowed that the project would be completed no later than April 2018. The MTA has announced several completion dates over the years, including one as early as 2010.
"I think [riders] have gotten so used to the date being pushed back," said LIRR Commuter Council chairman Mark Epstein, who attended the LIA meeting. "The target for completion has probably moved faster than most Long Island Rail Road trains."
MTA officials said in a statement that the analysis moving the date to 2019 is "preliminary" and they are looking for ways to mitigate possible delays.
Lhota said the delays come from complications in boring a tunnel under the busy Harold Interlocking in Long Island City, which is used by the LIRR, Amtrak, New Jersey Transit and freight rail operator New York and Atlantic Railway.
"It's the most complicated interlocking system anywhere in the United States and quite possibly the world, and we're tunneling underneath it," Lhota told the LIA audience. "To tell you it's complicated is an understatement."
Making the work even more difficult is the soft ground under the rail -- portions of which the MTA has had to freeze in order to dig through, he said.
Lhota added that the LIRR needs Amtrak workers' aid to carry out the East Side Access project, but federal officials want work on an unrelated project to build a train station at the James Farley Post Office building on Manhattan's West Side to be Amtrak's priority.
MTA officials have said they need to complete East Side Access by 2018 to keep $2.6 billion in federal funding. Lhota said yesterday he was not certain if that was still the case.
"We wouldn't go to 2019 if the feds said we can't do it. We'd just have to do something different," Lhota said.
The Federal Transit Administration has long raised concerns about the project falling behind schedule. In 2010, it called the situation "grim." Last June, it called the slow progress on some key contracts "unacceptable."
In January, the FTA said that overall construction on the project was only 43 percent complete by December -- short of the goal of 62 percent.
Given the project's benefits to Long Island, LIA president Kevin Law said the latest projection of delays "doesn't concern us."
"It's the biggest infrastructure project in the country. It's bound to have some delays because of all the complications," Law said. "They're doing everything they can to make it happen."