San Francisco’s already behind-schedule Central Subway won’t be completed until 2021, more than a year later than the city insists the line will be ready, according to a new report by the big dig’s main contractor.

Construction giant Tutor Perini Corp. also says the $1.6 billion project is running tens of millions of dollars over budget.

Tutor Perini laid out the delay troubles in an inch-thick binder that company representatives began circulating last week to San Francisco supervisors in the hope of enlisting their intervention in a contentious contract dispute with the Municipal Transportation Agency.

The company blames a string of “infrastructure delays” for the construction problem — including having to relocate Pacific Gas and Electric Co. power lines near the Chinatown station at Stockton and Washington streets and encountering harder-than-expected rock while excavating the tunnels.

Tutor Perini says those delays have added 15 months or so to the job, and that testing by another contractor once construction is finished will also take longer than planned.

If the firm is right, the first Metro trains won’t be running up to Chinatown until spring 2021 — well after both December 2018, which is what the city advertised when construction began six years ago, and the most recent target of late 2019.

It would also mean the rail line almost certainly won’t be ready for the scheduled fall 2019 debut of the Golden State Warriors’ new home in Mission Bay — leaving the 18,500-seat arena without a vital link to downtown for the team’s first two seasons in San Francisco.

The 1.7-mile subway, a crosstown extension of the T-Third Street line, will dive underground near the Caltrain depot at Fourth and King streets. Besides Chinatown, it will include subway stations at the Moscone Center and Union Square.

In October, an independent monitor concluded that the subway would be done in December 2019. That’s the estimate the city is sticking to.

“We are making great progress, and we are on track,” said Municipal Transportation Agency spokesman Paul Rose.

As for why he believes the monitor’s assessment is right? Rose said his agency “works closely with the (Tutor Perini) construction team on site, and they predict their portion will be completed by mid-2019, and that the line will go into revenue service by December 2019.”

Privately, other city officials think the company is trying to buttress its request for tens of millions of dollars extra that it says are needed to finish the job.

Tutor Perini, which has about half the project’s $1.6 billion contract, has submitted $112 million in change orders. Those are common in big projects, but the company’s request far exceeds the $79 million that the MTA set aside to cover them.

The two sides have established a special review board to consider each of the company’s 80-plus claims. Meanwhile, Rose says Tutor Perini is on the hook for $50,000 a day in penalties if it doesn’t meet the December 2019 finish date. The company has put workers on the job around the clock six days a week to try to make deadline.

Tutor Perini also takes exception to the city withholding $24 million of its payments for the roughly 60 percent of the job that’s been completed. While company officials did not respond to our request to be interviewed, in their report to the Board of Supervisors they branded the city’s action as “punitive and a violation of contract terms.”

Not so, countered Rose. He said withholding some payments is standard practice in large construction contracts and is intended only “to assure the project is completed as designed.”

It’s not the first time the city has fought with Tutor Perini. In 2002, City Attorney Dennis Herrera sued the firm for “artificially inflated” bills on the makeover of San Francisco International Airport, which ran more than $300 million over budget. Tutor eventually paid $19 million to settle the case, which cost the city $10 million in legal fees.

In an added twist, Maria Ayerdi-Kaplan, who was ousted last year as head of the agency overseeing construction of the Transbay Transit Center, was seen walking the corridors of City Hall last week on Tutor Perini’s behalf in the contract dispute. It was on her watch that the transit center went so far over budget that the Transbay Joint Powers Authority had to run to the city for a $260 million bailout loan.

One of Ayerdi-Kaplan’s ex-bosses on the agency board was none other than MTA boss Ed Reiskin, who has been pushing Tutor Perini to get the Central Subway built and opened on time and on budget.

Ayerdi-Kaplan did not return our call seeking comment.

San Francisco Chronicle columnists Phillip Matier and Andrew Ross appear Sundays, Mondays and Wednesdays. Matier can be seen on the KPIX TV morning and evening news. He can also be heard on KCBS radio Monday through Friday at 7:50 a.m. and 5:50 p.m. Got a tip? Call (415) 777-8815, or email matierandross@sfchronicle.com. Twitter: @matierandross