ALBANY — The Thruway Authority will spend $50 million over the next two years to repair the canal system after it was devastated by floodwaters from tropical storms Lee and Irene, according to its capital budget.

Flooding ruined dams and prompted the Erie Canal to close between Vischer Ferry and Amsterdam from September until late last month, when it opened for a brief season-ending stint.

Officials plan to spend $4 million dredging the canal over the section, as well as $14 million for repairs to Locks 7, 8, and 9. The work will begin next year.

The authority plans to spend $1.5 billion on maintenance and other repairs to the highway and canal it operates over the next four years, almost all of it financed with bonds.

Still, the 2012 amount is about $80 million less than last year, Thruway Authority Chairman Howard Milstein noted.

“We are mindful of Governor Cuomo’s historic effort to limit state spending, and although the authority receives no state aid, we intend to follow his lead to control operating costs and limit undue economic hardship on our customers,” Milstein said. “We have cut spending significantly in this budget, and we will restructure our operations to reflect the governor’s call for maximum government efficiency.”

Year-to-year operating costs are down six percent and there are fewer workers on the payroll, the budget shows.

It predicts slight increases in traffic, toll receipts and canal usage next year as the economy recovers.

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