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BOSTON — The Boston Globe reported that 83 percent of Massachusetts Bay Transportation Authority (MBTA) commuter trains left stations without the required number of conductors for at least 32 weeks last year, causing major problems with fare collections and contributing to nine consecutive months of declining fare revenues for the T, according to reports produced by Amtrak, which runs the MBTA’s commuter rail operation.

These unfilled or “blank jobs” are so pervasive that for 14 of those 32 weeks last year, excluding holidays, nearly all MBTA commuter train runs were understaffed, according to the reports by Amtrak, which operates the local commuter lines under a $150 million contract that expires next summer.

In addition, the T said yesterday, from late May to late June 2000 — and during nearly all of July that year — 71 percent of T commuter trains ran at least one conductor short.

When T officials found that out about a year later, the transit agency withheld $45,820 from Amtrak, the reports said. Authorities don’t know the amount of fares that went uncollected during that time.

The problem has been documented for the past three years, according to the MBTA. In April 2001, T director of rail operations Anna M. Barry told Amtrak she was concerned that a total of 912 jobs on trains had gone unstaffed from July 2000 to January 2001.

Amtrak officials never said a word and continued to bill the T for the empty jobs, which the T paid.

After discovering that Amtrak had not filled the jobs, Barry ordered the T to withhold $312,816 from its next payment to Amtrak, one of the largest penalties it has issued. Amtrak officials said they had no explanation for the problem.

“It is pretty well known that a level of staffing for the contract had been established, but why these positions were unfilled is a question,” said Amtrak spokesman Bill Schulz. “Inadequate train staffing resulting in uncollected fares is unacceptable. In the end, it’s Amtrak’s money, too.”

The blank job figures raise troubling questions about the T’s commuter rail service, which has recently come under fire for lax fare collection and a series of operational lapses, including a passenger who had a heart attack on a train that did not stop for the emergency. He later died.

The fare collection problem has led T officials to station “spies” on commuter trains to see if conductors were collecting all tickets and fares.

This week, MBTA officials are expected to receive bids from at least three private competitors who want to take over the commuter rail operations contract from Amtrak when the contract expires. New provisions in the contract include financial incentives to collect full fares and a penalty of $500 for each position not adequately staffed. The new contract also calls for a crew-to-passenger ratio of 1 to 300, said T spokesman Joe Pesaturo. Should T officials find that a trip is not adequately staffed, it can penalize the new carrier $10,000.

Amtrak CEO David Gunn has said the national rail carrier, which has run the MBTA commuter line — one of its most lucrative operations — since it began, won’t bid on the new contract. Gunn said the MBTA’s new terms would place too many restrictions on the debt-ridden national rail carrier.

Officials say trains end up understaffed for a variety of reasons — sick calls, classes, or the effect of federally-mandated rest time for conductors after they have worked a certain number of hours. Amtrak officials are finding it cheaper to let the trains run understaffed than pay overtime to staff them, T officials said.

During peak runs, MBTA commuter trains are supposed to operate with a conductor and two assistant conductors to handle ticketing and direct the loading and unloading of passengers. On the popular Attleboro line, the trains typically run with a conductor and three assistants.

Off-peak runs usually use one conductor and one assistant conductor, said Steve Jones, the T’s commuter rail director.

Passengers have complained for years about buying expensive monthly passes only to have no one check them on the train. At the same time, other passengers have gotten free rides by squeezing out as many as 20 round trips from a cheaper, 12-ride ticket, courtesy of inattentive conductors.

When Kevin Lydon, the popular director of commuter rail for Amtrak in Boston, was fired last month, Gunn said the MBTA’s commuter rail work force is overstaffed, files nearly a quarter of all injury claims in Amtrak’s Northeast Corridor, and pays more overtime than any other Amtrak operation.

Charlie Moneypenny, chairman of Commuter Rail Workers United, a consortium of labor groups, said the understaffing is the result of Amtrak orders to cut back on overtime.

“It doesn’t surprise me because they’re blanking positions everywhere,” Moneypenny said.