These days, even a common cold can disrupt the Massachusetts justice system.

It happened just over a week ago, when an assistant court clerk was sick, forcing the short-staffed Suffolk Superior Court to combine two criminal sessions to accommodate a cramped schedule. The clerk for civil courts said he similarly fears a “mad scramble” to staff court proceedings when anyone on his team is out.

“Every day it depends on what our staffing is,” said Maura Hennigan, the clerk-magistrate for criminal business in the Superior Court that covers Boston. “We don’t know how long we’re going to go on like this.”

And the staffing shortage, triggered by a state-imposed hiring freeze, is but one of several financial problems piling onto the court system, ratcheting up tensions in a part of government

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