To plug a gaping hole in the state budget created by the collapse of a $1.6 billion labor agreement, Gov. Dannel Malloy recommended Wednesday nearly 5,500 layoffs of state workers and $54 million in reductions to state aid to cities and towns.

The recommendations come one day before a special session Malloy called last week, when it became clear that a deal on labor concessions reached with state union leaders in May would be rejected by union membership. While 11 of the 15 state unions and nearly 60 percent of state workers overall voted to approve the agreement — which included a pay freeze and concessions on retirement and health benefits — labor leaders needed a self-imposed threshold of 14 unions and 80 percent overall approval for ratification.

In the absence of the deal’s $1.6 billion savings over two years, Malloy released a plan to cut $700 million in the budget’s first year, which starts Friday, and $900 million in the next year. The cuts amount to the elimination of 6,466 state employee positions, about 1000 of which are currently vacant. $54 million would be cut from the state’s grants to municipalities, of which New Haven is the second-largest recipient.

“Working with the legislature, we will have a balanced budget and one that, while making painful cuts and difficult decisions, will be balanced honestly without tricks or gimmicks,” Malloy said in a press release.

While it is unclear what portion of the city’s budget will be affected by the cuts, city officials will have to address the shortfall through either deeper reductions to the city workforce, cuts to city services or increased property taxes.

In order to execute his plan, Malloy will first need to obtain expanded rescission authority from the General Assembly, which denied him that right during the regular legislative session. With just two days until the new fiscal year, legislators in Hartford have indicated that they would be willing to grant Malloy the power necessary to make the cuts at the special session tomorrow, the Connecticut Mirror reported.

Meanwhile, labor leaders, who said they are in an “unprecedented situation,” have struggled for the past several days to find a solution to the sudden budget gap that avoids mass layoffs.

“Simply rejecting the agreement poses an extreme risk not only to the democratic will of the majority, but the services we provide to the public, and to the economic recovery upon which ultimately all of us depend,” union spokesman Matt O’Connor said in a statement. “Accepting the agreement over the adverse votes of the members of four of 15 voting units under the current rules is also unacceptable.”

Leaders of the State Employees Bargaining Agent Coalition (SEBAC), the coalition that negotiated the deal with the Malloy administration on behalf of all 15 unions, will examine whether the voting threshold, in effect since 1996, is still appropriate, O’Connor said.

The special session begins at 10 a.m. tomorrow. Check back tomorrow for more coverage.