An LIRR train disappears into a tunnel under the 49th...

An LIRR train disappears into a tunnel under the 49th Avenue underpass in Hunter's Point. (May 11, 2011) Credit: Craig Ruttle

Amtrak owns and maintains the tunnel where one of its trains was derailed, crippling Long Island Rail Road service to and from Penn Station this week. But the LIRR is likely to be handed the repair bill.

To critics of LIRR's relationship with Amtrak, that would be adding insult to injury.

A "joint facilities agreement" signed in 1988 requires that the LIRR, as the primary user, cover most of the cost of maintaining the tracks from the East River tunnels to Penn Station. Amtrak employees do the work.

"The arrangement is crazy, and it cries out for a rational redo," said Patrick Foye, one of several Metropolitan Transportation Authority board members who have called for the LIRR to take over maintenance work now performed by Amtrak from the East River tunnels to Penn Station.

"This deal has to be blown up and started all over again," said MTA board member Mitchell Pally.

LIRR officials pointed out that the agreement allows for negotiation of repair costs in some incidents, depending on the LIRR's liability.

Neither the LIRR nor Amtrak would estimate the cost of repairing the rail, track bed and 282 wood ties damaged when a 60-mph Amtrak train came off the tracks in the tunnel Sunday afternoon. "Right now we are focused on getting service back for our customers," LIRR spokesman Joe Calderone said.

Pally said he expected the tab would be in the "hundreds of thousands of dollars," adding, "It may even go over a million." Former MTA chief financial officer Gary Dellaverson declined to offer a prediction, but said he doubted it would be less than hundreds of thousands.

Dellaverson said he expects the LIRR won't be so quick to write a check. "There will be a debate between the two properties about that, and it will have to do with what caused [the derailment] and who was responsible and whether there was any negligence," he said.

Amtrak declined to comment, other than to confirm that under the lease agreement the LIRR covers all maintenance costs for two of the four East River tunnels, and some percentage of the maintenance costs of the other two. The affected tunnel is one of those LIRR is responsible for.

The derailment has not seriously affected Amtrak service.

But it has caused major disruptions on the LIRR since Monday, with more than a score of cancellations each day and frequent delays. Officials say they expect LIRR service to be back to normal Friday morning.

The LIRR paid Amtrak $8.7 million in maintenance costs last year, including $1 million for "extraordinary maintenance," such as emergency repairs, according to the LIRR.

Former LIRR president Bruce McIver, who signed off on the 1988 deal, said the rationale was that, as the primary user of the East River tunnels, the LIRR should bear most of the maintenance cost. But, because Amtrak owns the facility, it would be responsible in carrying out the maintenance work.

"I suspect, part of this had to do with the unions. Amtrak did not want to give up the right to maintain their property," said McIver, who defended the agreement.

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