MANKATO — The most delayed state budget in Minnesota history faced another delay even after lawmakers were called into special session at 3 p.m. Tuesday.

At 6 p.m., the House and Senate chambers remained quiet, and Rep. Tony Cornish explained why.

“We’re counting noses,” said Cornish, R-Good Thunder. “We’re just making sure we have enough votes on all nine bills and the bonding bill.”

When the House and Senate reconvened a short time later, five bills  — to provide two more years of funding for colleges, criminal justice programs, transportation, state parks and jobs programs — were debated and quickly passed. Virtually all Democrats opposed the bills, but Republicans control the House and Senate and maintained enough unity to get the first bills passed.

Still waiting were controversial K-12 education and tax bills — the ones that will provide $1.4 billion in non-tax revenue through delayed payments to schools and the sale of tobacco bonds — along with funding for state agencies and health and human services.

It was that additional $1.4 billion that brought an end to the budget impasse between legislative Republicans and Democratic Gov. Mark Dayton, but lawmakers on both sides found plenty to dislike about what they considered accounting gimmickry.

Rep. Kathy Brynaert said the deal to add $1.4 billion to the $34 billion budget originally passed by the Legislature — and vetoed by Dayton — eased some of the most onerous reductions in the original bills.

“There’s some improvement in  lot of these bills,” said Brynaert, DFL-Mankato.

But Brynaert said it would have been hypocritical to support the spending bills when she knew she would vote late Tuesday or early Wednesday morning against the school-payment shift and the tobacco bonds, which borrow $700 million against future payments to be made by tobacco companies as part of a settlement of a state lawsuit in the 1990s.

In other cases, the cuts in the spending bills were insupportable for Brynaert.

The higher education bill will bring tuition hikes and reduced class offerings to students at Minnesota State University, South Central College and other colleges around the state, she said.

“It really dramatically affects students,” Brynaert said. “It dramatically affects families because of the costs. A lot of people consider that a form of a tax increase.”

Democrats mostly restricted themselves to one or two members speaking against the bills, with Rep. Terry Morrow — a St. Peter Democrat and Gustavus Adolphus College professor — handling the duty on the higher education bill.

Morrow focused on Republican Rep. Bud Nornes’ comment that there would actually be a slight increase in revenue in the next two years for the University of Minnesota and the Minnesota State Colleges and Universities.

“It’s coming out the pockets of the undergraduate students going there,” Morrow said.

State aid to the colleges is being cut by “historically large amounts” — 13.5 percent for MnSCU — and tuition will make up the difference, Morrow said. That puts college educations at risk for some families, which means future educated workers won’t be there for Minnesota businesses.

Cornish was prepared to vote for all of the budget bills and was confident a sufficient number of his Republican colleagues would join him to get the entire budget to Dayton, who agreed to sign all of the bills if lawmakers managed to pass them all.

Many GOP lawmakers dislike the shifts and borrowing, many didn’t want to go a penny above the $34 billion in their original budget, and many didn’t want to drop some of the contentious policy provisions that Dayton insisted be removed, Cornish said. At the same time, there are no state-level tax hikes in the bill and overall state spending is being restrained in a way that hasn’t been seen in half a century.

During a meeting of Republican House members, the five-term veteran told younger colleagues to accept victory, recognizing Dayton needed to win something as well.

“How could we be so naive to think we’d get everything we want and the governor was just going to roll over? That’s what I said in my speech,” Cornish said.

Still, there was one moment of drama in the Senate on one of the first five budget bills. Ruing the loss of a provision banning stem-cell research at the University of Minnesota — a provision strongly supported by Minnesota Citizens Concerned for Life — several Senate Republicans voted against the college-funding bill or withheld their “Yes” votes.

For nearly 10 minutes, the vote was held open before a sufficient number of Republicans relented and the bill passed 35-30.

With that bill passed, Morrow expected the other pieces of the budget to fall into place.

“I think the higher education bill was the one where they were going to have the problem,” Morrow said.

Just before 10 p.m., the House took up the tax bill and Democrats leveled some of their harshest criticism of the night. Morrow, in an interview just before the session resumed, said selling tobacco bonds to cover day-to-day operational costs is a bad precedent.

“It’s like using the credit card to buy groceries,” Morrow said. “Next month you have to pay the credit card bill and you still have to buy the groceries.”

The deal worked out between Dayton and legislative leaders on Thursday, unpopular as it is on both sides of the aisle, provides a route to ending the shutdown. That’s become increasingly critical for many Minnesotans, and defeating any of the bills in search of a better deal would be dangerous, Cornish said.

“I think that would probably be the worst thing that could happen,” he said. “Because there is no Plan B right now.”