House Speaker J. Brendan Sharkey, D-Hamden, and the administration of Gov. Dannel P. Malloy engaged in an extraordinary exchange of criticism Friday over two fiscal controversies, ratcheting up intra-party tensions over how to resolve a worsening budget shortfall.

Sharkey told reporters after a House Democratic majority caucus that his members blame Malloy for the raises the University of Connecticut offered to non-teaching staff, and they object to the administration’s suspension of $140 million in payments owed to acute-care hospitals.

Sharkey said the caucus resented Malloy’s public demand that they reject the proposed UConn contract, which was withdrawn by the university and union Friday in the face of its certain rejection by the legislature.

The speaker suggested that the governor, a fellow Democrat, was negligent in not directing his appointed university trustees to negotiate a contract the administration views as affordable.

“It was only in the 11th hour when we were considering a vote that the governor weighed in,” Sharkey said. “I’d also hoped that if the governor has concerns about these contracts that he step in a little bit earlier and not expect the legislature to solve all these problems at the 11th hour.”

Malloy not only is the appointing authority for nearly every trustee, but can participate in their discussions as the ex-officio president of its board. He did not attend the February meeting where the trustees unanimously adopted the contract.

The administration responded in kind to Sharkey, accusing the speaker of being unable to muster sufficient House votes for a recommendation to kill the contract when it came before the Appropriations Committee.

“The fact is, unlike Senate Democratic leadership, the speaker was unable to muster votes against the contract in Appropriations, despite his best personal efforts,” said Mark Bergman, the governor’s deputy chief of staff.

Bergman said Sharkey’s criticism of Malloy was meant to obscure his own difficulty in leading the House majority to reject the contract.

“Now he’s trying to deflect attention away from his own inability to manage his caucus,” Bergman said. “The simple reality is that the governor’s intervention is what led to this contract being withdrawn. The speaker should stop looking for other people to do his own heavy lifting.”

Sharkey declined to respond to Bergman, said his spokesman, Gabe Rosenberg.

Roy Occhiogrosso, a top aide during Malloy’s campaigns in 2010 and 2014, suggested the administration was pushing back hard at Sharkey, because his complaint was directed at the essence of the governor’s political brand.

“People have accused Dan Malloy of many things. Being weak would not be one of those things. Being somebody who is afraid to make tough decisions would not be one of those things,” Occhiogrosso said.

The House and Senate were prepared to vote on rejecting the deal when UConn and the University of Connecticut Professional Employees Association, an AFT affiliate representing the employees, agreed to withdraw the proposed contract. Union leaders said the version before the legislature contained two errors.

It was unclear Friday if new negotiations would involve substantive changes to the contract or simply correct the technical deficiency: Errors in an index common to contracts that states its provisions prevail if contradicted by other state laws.

That deal would have given 1,900 non-teaching staff at UConn annual raises of between 3 percent and 4.5 percent at an estimated cost to the state and university of an additional $94 million over five years. The union agreed to extend its members’ work week from 35 hours to 40 hours.

“It’s their contract, and they get to decide how it’s going forward,” said Jan Hochadel, president of AFT-Connecticut. “They might actually decide that they know the economic climate that we are in and decide to start over again. That is completely up to them.”

Union leaders joined legislators in taking issue with the governor’s handling of the contract.

“If he had expressed those concerns six months ago, two months ago or even one month ago, then it wouldn’t have had all this negative focus on it. For him to come out at this late hour, it was very frustrating to a lot of people,” said Lori Pelletier, the head of the Connecticut AFL-CIO.

House and Senate Republican leaders said the “glitch” was a face-saving pretext to avoid a vote by the legislature.

Senate Minority Leader Len Fasano, R-North Haven, said a corrected copy was filed with the Senate clerk two days ago. Fasano and House Minority Leader Themis Klarides, R-Derby, said they believed Democrats were happy to avoid a vote.

“The fact is there was not support for this contract, so the Democrats came up with a last-second ‘glitch’ in the contract and avoid exposing their members to a vote,” Klarides said.

“This is the same dance we see Democrats and union leaders go through every time they want to avoid standing up and answering to the people of this state,” Fasano said. ” I just worry that this same contract will be held and won’t come up again until after the elections in November, when there’s less public pressure to vote down this contract.”

But Senate President Pro Tem Martin Looney of New Haven and Senate Majority Leader Bob Duff of Norwalk, both Democrats, said in a joint statement: “No matter the excuse they’re using to withdraw the contract, the fact remains that the contract was going to be defeated by the Senate Democrats.”

Contracts and arbitration awards automatically take effect in the absence of a negative vote by one chamber of the General Assembly. The last rejection was a Senate vote in 1997 that killed an arbitration award involving a contract with correction officers.

The issue of the UConn raises quickly receded in light of the volley of criticism exchanged by the administration and the speaker, whose cooperation will be crucial in negotiating revisions to the second year of a biennial budget approved last year.

Sharkey, who was joined by House Majority Leader Joe Aresimowicz, D-Berlin, in addressing reporters, made clear that he and other legislators viewed Malloy’s demand on the UConn contract as a breach of Capitol protocol.

“He could have very easily communicated in the same public way that he did earlier this week to the Board of Trustees that this is something that he would not support,” Sharkey said. “My only point is that I don’t think any speaker ever appreciates having any governor weigh in on our affairs, particularly in this case. This is something that was in the governor’s court to address much earlier than he did.”

Malloy faces bipartisan opposition on hospitals

In response to a question, Sharkey also challenged the administration’s authority to unilaterally withhold the hospital reimbursements against the clear wishes of the legislature, and he urged Malloy to reconsider his decision Thursday to withhold them in the face of growing deficit projections.

The industry originally was budgeted to pay $556 million in taxes and receive $256 million in reimbursements. In mid-September, the administration cut some payments and withheld others. At that point, the industry expected to receive just $64 million back against $556 million paid to the state.

In a December special session, legislators reversed some of the September cuts and reached an understanding with Malloy to release the withheld payments — all of which elevated this fiscal year’s payments to the industry to $164 million.

The latest action by the administration suspending about $140 million in payments now leaves hospitals slated to receive $22 million in tax reimbursement payments this fiscal year — or just 4 percent of what they will pay.

“It was not what we negotiated,” Sharkey said, referring to the agreement in December. “This was something we fought very hard for as legislators to ensure that these funds would be available to our hospitals. Withholding them is unacceptable, and we are all calling on [the administration] to release those funds as soon as possible.”

Looney concurred.

“These cuts will have a potentially significant impact on patient care and the workforces of these facilities that are in many cases the largest employer in a community,” Looney said. “During the December special session, Democrats in the General Assembly successfully fought to provide funding in the face of Republican opposition.”

Fasano said Looney was misrepresenting the record: The GOP opposed the hospital cuts.

“We continue to support hospitals today which play a vital role in our health care system,” Fasano said. “Any further cuts will have an adverse effect on care for the poor, sick and elderly. Holding back this funding skirts a core responsibility of government to care for those most in need.”

Bergman said the legislature will have to find offsetting cuts if they want to make the payments to the hospitals.

“Leadership is about choices – do you cut more from social programs that serve those who need it most, or do you cut more from hospitals that are seeing soaring profits?” Bergman said. “You cannot be for all things, all the time.”

Correction: The original post referred to the last rejection of a labor deal occurring in 1987, not 1997.