A labor union representing nearly 40 percent of the state court system’s workforce has overwhelmingly approved a new contract providing a 6 percent pay raise over the next two years.

Members of the Civil Service Employees Association (CSEA), who have been working without a contract for the past three years, voted two-to-one in favor of a proposed pact that would result in raises of 2 percent on Oct. 1 of this year, April 1, 2015 and April 1, 2016, plus a $750 bonus payable March 31, 2017.

The contract, which is subject to approval by the Legislature, also includes: a restructuring of the longevity bonus program; new provisions on seniority; an expedited disciplinary process for alleged time and leave violations; and a contingency for a lag payroll of up to two days in the 2015-16 and 2016-17 fiscal years if the court system budget is rejected by the Legislature and governor.

“This was a very difficult negotiation, and I am proud that CSEA members ignored outside noise and focused on the facts about his agreement,” CSEA President Danny Donohue said in a statement. Chief Administrative Judge A. Gail Prudenti has said the agreement “balances the state’s ongoing fiscal constraints with the desire to provide increased compensation and benefits for the court system’s hardworking employees.”

The CSEA represents about 5,700 of the 15,000 non-judicial employees of the Office of Court Administration, the vast majority of them upstate. It is the largest of the 12 unions representing court system employees.