It also said in its statement that last month it had “sought the inspector generals from both the U.S. Railroad Retirement Board and from the M.T.A. to review this matter.”

On Sunday night, the railroad released another statement, saying that it would cooperate fully with any investigation by Mr. Cuomo. “We will provide any information requested,” the statement said.

The L.I.R.R.’s disability rate has been three to four times that of the average railroad in recent years, and far outstrips Metro-North, which serves commuters north of New York City and has a work force of about the same size. For example, from 2001 through 2007, Metro-North had 32 cases of disabilities resulting from arthritis and rheumatism, compared with 753 at the L.I.R.R.

The disability problem has been compounded by labor contracts that allow longtime workers to retire with a pension as early as age 50 and by a tangle of negotiated rules that allow workers to reap four days of pay for a single day’s work. Such rules allowed eight senior train engineers to earn from $215,000 to $277,000 in 2006.

While the federal government pays disability claims, a significant burden falls to taxpayers. Passengers could face another fare increase, and the Metropolitan Transportation Authority is seeking half a billion dollars a year from taxpayers to close a huge budget gap, as the railroad grapples with the cost of overtime, training replacements and early pension payments.

Mr. Paterson’s quick action comes as the state faces a $26 billion deficit over the next three years and expects a calamitous decline in tax revenue because of the financial woes that have buffeted the financial industry. The governor has made fiscal discipline the centerpiece of his six-month-old administration.

He will ask the inspector general of the transportation authority to specifically examine whether supervisors and soon-to-be-retiring staff members at the Long Island Rail Road are conspiring to inflate paychecks in retirement. Disability and pension payments are determined partly by what an employee earns in the five years before retirement.