Just hours after the House dealt a blow to Gov. Dannel P. Malloy’s criminal justice reform on Thursday, the governor cut $20 million in local aid from the state budget to offset savings he had expected from the reform bill.

Lawmakers traveled to Hartford on Thursday for a special session to vote on Malloy’s Second Chance Society proposal to eliminate the cash bail system for nonviolent misdemeanors. Instead, their agenda was sharply curtailed, only passing the annual bond package of construction projects unanimously before adjourning.

The state budget factored in millions of dollars in savings based on the assumption that Second Chance would be approved. With the reform not passing, “the budget would be out of balance” if adjustments were not made, Malloy wrote in his line-item veto message that included the $20 million aid cut. It also included slashing $1.7 million for CT Humanities and $775,000 in payments to federally qualified health centers, typically used by low-income clients.

Senate Republican leader Len Fasano of North Haven said the cut will cause concern in cities and towns, which have largely approved their budgets in advance of the new fiscal year on July 1.

“This is just going to cause property taxes to go up,” Fasano said. “Municipalities have already locked in their budgets.”

City and towns already were dealing with reductions in municipal aid, many of them having to redraw budgets to reflect lower amounts.

New Britain Mayor Erin Stewart, whose city passed a budget Thursday night with higher taxes following concerns about state aid, said it was not clear how the latest cuts would affect her city.