With a gross salary of more than $333,000, BART’s highest-paid employee last year wasn’t its general manager, police chief or a worker who racked up gobs of overtime scrubbing grime from filthy train seats.

It was someone who did no work at all for BART in 2012: Dorothy Dugger, the agency’s former general manager who resigned under pressure more than two years ago.

Under a lucrative retirement scheme, Dugger, 57, quietly stayed on the books, burning off nearly 80 weeks of unused vacation time, drawing paychecks and full benefits for more than 19 months after she agreed to quit in May 2011, according to an analysis by this newspaper. By remaining on BART’s payroll, she accrued almost two extra months of vacation, while sitting at home drawing a six-figure salary for unused time off.

The months of extra pay were on top of the $920,000 that BART paid Dugger to leave after the agency’s board botched an effort to fire her by violating public meetings laws.

“Wow,” said James Fang, a BART board member who tried to oust Dugger. “She was still on the payroll? I did not know this. It’s startling.”

In 2012 alone Dugger’s gross pay could have bought 52,837 round-trip BART tickets between downtown Oakland and San Francisco’s Financial district. She even received more pay than the person who replaced her to run the Bay Area commuter railroad, General Manager Grace Crunican, who took home $316,000.

Without leaving her home in Oakland’s Crocker Highlands neighborhood, Dugger reaped the astonishing windfall by cashing in more than 3,100 vacation hours, saved during her 20 years with BART.

Many cash-strapped public agencies are now under scrutiny for allowing departing employees to convert huge banks of unused vacation and sick time into big cash payouts, but a little-known policy in BART’s rules for senior managers like Dugger made her perk even sweeter.

Because she was allowed to drag out her vacation-bank payments for months, Dugger received $138,000 worth of benefits, including pension contributions and medical insurance — perks she would not have received if she had taken her vacation payments in a lump-sum check. Since she remained on BART’s payroll, Dugger also received an additional $98,000 in cash, because she was still racking up vacation time and management bonuses — even though she had no one to manage.

That alone was more than the 2012 gross pay of almost three-quarters of BART’s 3,340 workers, the agency’s compensation data shows.

Remaining on BART’s payroll also added both time and money to the calculations on which Dugger’s retirement is based — increasing her pension payments by more than $1,000 a month for life. When her time on BART’s books finally ran out in December, she began to draw a pension of $181,000 a year.

Reached this week by phone, Dugger said she was entitled to the money because she earned the time off.

She said her decision to spread out her unused vacation payments after her four-year tenure as general manager ended in May 2011 “best suited my needs. I made that decision some time ago. I don’t remember every factor.”

BART’s vacation policy requires senior managers to decide every year whether they want to save unused time off for a retirement bonus. They must place the time in an account that can only be cashed out at the end of a career.

Not taking a lump sum on top of her $920,000 settlement eased Dugger’s tax burden, as well.

But news of her bounty wasn’t easy for BART riders to stomach.

“I hope it becomes a big stink,” said BART patron Mitch Roland, of Alameda. “This is an agency funded by taxpayers. … They should have stricter controls.”

Crunican, the new general manager, didn’t respond to several messages left with her spokeswoman last week. BART board President Tom Radulovich, of San Francisco, did not return several phone calls.

BART board member Robert Raburn, of Oakland, said Dugger’s payout shows a serious problem in how the agency deals with unused time off.

“We should be able to control it,” he said of time accruals. “It should be use it or lose it.”

Another board member had concerns.

“We have to look at this,” Fang said. “We never think about these very critical and important little things.”

BART is widely known for offering some of the most lucrative government benefits and sweeteners in California. Employees contribute nothing to pension costs, the agency provides rare deferred compensation accounts as an extra retirement fund and most employees contribute only $92 a month to medical insurance costs no matter how many dependents they have on a policy.

But Dugger appears to have especially benefited. The value of the time off she stored up before becoming general manager skyrocketed when she ascended to the top job in 2007 and received a raise of nearly $100,000 a year, records show. She was paid for all 3,100 hours of unused time off at her final, highest pay rate, she said, not her rate when the time was accrued.

“It was time (off) I earned my whole career at BART,” she said. “It’s a cost of having the option” to save the vacation until the end of a career, she said.

When asked if she thought that was fair to BART riders, she said: “That’s a fair issue to debate.”

Raburn was one the directors who voted to fire Dugger in early 2011 after mounting complaints about service and cleanliness of the aging transit system and criticism that she failed to provide strong leadership after the 2009 fatal shooting of a handcuffed African-American man, Oscar Grant III, by a BART police officer.

But the directors were forced to quickly rescind that decision after discovering they had not followed public notice requirements to schedule the closed-door meeting to vote on Dugger’s ouster. Dugger threatened to sue, and the board agreed to pay her $920,000, plus $14,000 in legal costs, to drop the threat and resign.

“We had to buy her out, I don’t know what else we can say. It could have been much worse if she had gone to court,” Raburn said.

But lost in that was any discussion of how to deal with all of Dugger’s vacation time. “I can’t talk about what we discussed,” Raburn said.

Dugger said she was proud of her time with BART. Asked if her lucrative use of vacation time exposed a fiscal flaw in the agency, she said, “I think BART’s track record on fiscal management is quite solid.”

Contact Thomas Peele at tpeele@bayareanewsgroup.com. Follow him at Twitter.com/thomas_peele.