ALBANY, N.Y. — For years, Gov. Andrew M. Cuomo and some Democratic leaders have had an antagonistic relationship with the left-leaning Working Families Party, a labor-backed group whose increasing influence and independence have only widened the divide.

So when Mr. Cuomo and state leaders decided this year to expand a public campaign financing commission’s authority — giving it a mandate to rewrite election laws affecting smaller political parties — the independent party’s leaders feared the worst.

On Monday, their concerns were realized: The commission approved a slew of changes that will make it harder for political third parties to survive in New York.

By a 6-3 vote, the commission voted that in order for political parties to maintain a guaranteed line on the state ballot, they must draw either 2 percent — or 130,000 votes — of the general election vote for governor or president every two years.

In 2018, the Conservative Party was the only third party to receive more than 130,000 votes in the New York governor’s race; the Working Families Party, with Mr. Cuomo at the top of their ticket, received some 114,000.

The current threshold is 50,000 votes every four years, pegged to the governor’s race, a level that regularly allowed multiple smaller parties on both ends of the political spectrum to qualify for state ballots.

Should a third party fail to garner the required number of votes, it can still regain a ballot line for a candidate through petitions.

But the commission agreed to make that process harder, too: It voted to raise the number of signatures required to petition onto the ballot to 45,000, from 15,000.

The commission’s decisions, to be finalized in report due by Dec. 1, will become law unless the State Legislature holds a special session before the end of the year to modify the panel’s plans.

The decisions, made during a contentious meeting in Westchester County, were met by angry responses from audience members, who booed and shouted “Shame!” at the nine-person commission. The de facto chairman, Jay Jacobs, the leader of the New York State Democratic Party and a close ally of Mr. Cuomo’s, was a particular target of the vitriol.

Several audience members were removed after commissioners complained they were disturbing the meeting, which did not allow for public comment.

“You’re doing the governor’s bidding!” yelled one protester.

The idea of raising the threshold had drawn opposition from national leaders, including Senator Elizabeth Warren, a top Democratic candidate for president, who said on Twitter on Monday morning that “manipulating the rules” to attack the Working Families Party and “push them off the ballot is wrong.”

The new thresholds were also condemned by Working Families leaders in New York, who angered the governor last year by backing an unsuccessful primary challenge to Mr. Cuomo by the actress Cynthia Nixon.

“Governor Cuomo and Jay Jacobs were hell bent on punishing the W.F.P. for our independence,” said Bill Lipton, the party’s New York director, who called the new ballot qualification requirements “a clear abuse of state power to advance the governor’s political agenda.”

Rich Azzopardi, a spokesman for Governor Cuomo, a third-term Democrat, said that the commission comprised appointees from State Senate and Assembly leaders, and “only two were from the executive.”

“We will review the report,” Mr. Azzopardi said. “And believe these paranoid rants should be taken for what they are.”

The controversy over the new limits overshadowed the commission’s adoption of a plan to use public money to amplify donations of up to $250 to candidates for statewide and state legislative races, putting emphasis on the small-dollar giving that has propelled some progressive candidacies.

Such a tiered-matching program — beginning at a 12-to-1 match for the smallest donations — could mean $2,300 for a $250 contribution in state legislative races, according to Reinvent Albany, a government watchdog group.

The commission also voted to lower the contribution cap for statewide candidates to $18,000 from its current level of up to $69,700, though such limits remained among the highest in the country.

“Unfortunately, while better than the abominable status quo, the commission’s proposal does not reduce the dominance of big money enough,” said a spokesman for Reinvent Albany, Alex Camarda.

Despite such caps and advances in public financing — long a goal of progressive activists — officials with good government groups were left shaking their heads at how the commission arrived at its decisions after fractious public hearings and what they say were secret back-room negotiations.

“The public hasn’t seen any language. This commission has been operating largely out of sight, and it appears that the only feedback they react to is from governor and legislative leaders,” said Blair Horner, the executive director of the New York Public Interest Research Group.

Indeed, the commission often seemed to be changing its mind on issues mid-thought: At one point on Monday morning, the panel rejected a proposal to raise the contribution limit for races in the Assembly. Minutes later, after the arrival of one of Mr. Cuomo’s appointees, Mylan L. Denerstein, the commission took up the proposal again and passed it.

In one victory for small parties, the commission did not eliminate so-called “fusion voting,” which allows candidates to collect votes on multiple lines, including third parties, thus helping those parties meet the thresholds for staying on the ballot.

As the group’s deadline approached and third parties’ existential anxieties peaked, Senator Chuck Schumer, along with three New York Congress members, urged the panel to leave the practice alone. Mr. Cuomo had expressed measured support as well, saying he had benefited from fusion voting, which is allowed in only a handful of other states.

Leaders of the state Conservative Party, which seemed better positioned to survive a new 2 percent threshold, nonetheless also attacked the commission, questioning its constitutional authority.

“This is a classic example of government engineering a crisis and then presenting an impossibly bureaucratic solution to it on the backs of taxpayers,” the party chairman, Gerard Kassar, said in a statement.

Supporters of the new qualifying numbers for political parties said that they were necessary to prevent the spiraling costs to taxpayers — who would now shoulder part of candidates’ expenses via public financing, including in primaries — as well as updating thresholds that were established in the 1930s.

In his closing remarks, Mr. Jacobs defended the commission and spoke directly to attendees who “appeared so angry.”

“I am trying to the best that I can, as one member, to build a system that will be fair, balanced sustainable and effective,” Mr. Jacobs said, adding that he understood that dissent was part of democracy. “I at no point meant any disrespect to anyone.”

Vivian Wang contributed reporting.

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