Despite the conclusion of one of the more controversial contract battles in recent history between the Civil Service Employees Association and the executive branch, Gov. Andrew Cuomo and NY’s largest state workers union remain at odds over a host of issues.

The 66,000-member union approved a five-year contract with the state that includes two years’ worth of furloughs, increased costs for health insurance and wage freezes for two years.

The labor agreement passed, 16,896 to 11,856, CSEA said.

The agreement is a major victory for Cuomo, who sought to gain concessions from unions. And it’s a victory for CSEA President Danny Donohue, who negotiated deal that averted 4,500 layoffs.

But it was evident tensions were high during the negotiating process. Donohue said today Cuomo’s negotiating approach “could have been better. He revealed the administration initially wanted a six-year contract “with a lot more zeroes.”

The union, which declined to endorse Cuomo or his Republican opponent, Buffalo businessman Carl Paladino, last year, still is not thrilled with the second floor.

At a news conference this morning, Donohue reiterated labor’s support for a continuation of the so-called “millionaires tax” – a surcharge on those making $250,000 or more that is set to expire at the end of the year.

Cuomo sided with the majority of Senate Republicans during the 2011-12 budget contretemps when it came to extending the surcharge as a way of closing the $10 billion deficit over union and liberal lawmakers’ objections.

Donohue also repeated his stance on the proposed Tier VI, a less-generous pension tier designed to save $90 billion over the next 30 years.

“Tier VI is crazy in our opinion,” he said. “They introduced Tier V last year. We think that’s far enough at this point.”

The threat of new layoffs, despite the labor agreement, still hangs over CSEA. Donohue said he would watch the SAGE Commission, the panel charged with reducing and reorganizing state government, very closely.

But he said it would not be to Cuomo’s political advantage to lay people off – especially in the middle of what could be a double-dip recession. “I don’t think the governor really wants to lay people off,” Donohue said.

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