Republic Airways Holdings Inc. said a worsening pilot shortage is forcing it to cut its flying for big U.S. airlines, hurting the regional carrier's profits and sending its stock plummeting by half.

Republic, which flies about 1,250 flights a day for big U.S. airlines, said it had reduced flying by 4% in the second quarter and is discussing further cuts with its airline partners through the first half of 2016—some of the biggest tangible effects of a pilot shortage in the U.S.

Shares in Republic were down about 53% in midday trading Monday, near a three-year low, and off more than 70% this year.

Republic attributed its problems in part to a series of new government rules. In August 2013, the Federal Aviation Administration raised the minimum flight experience required for most commercial passenger pilots to 1,500 hours from 250, increasing the time and cost to become a pilot. In January 2014, the agency also began requiring more rest for pilots, reducing their productivity by 5% to 7%, Republic said.

Republic said in a news release late Friday that those changes, combined with an ongoing labor dispute with its pilots, are leaving it with too few aviators to fly the schedules demanded by its three airline partners, American Airlines Group Inc., United Continental Holdings Inc. and Delta Air Lines Inc. Republic said it expects to shrink its fleet as a result.

Regional carriers like Republic operate roughly half of all domestic flights in the U.S. and carry about a fifth of the passengers. Republic is nation's second-largest regional carrier, after SkyWest Inc.

There is much debate within the U.S. airline industry over what is causing the tight supply of pilots. The major pilot unions have said there is no shortage of qualified pilots, only a shortage of those who are willing to work for the low pay the airlines offer.

The major airlines have said they aren't struggling to find pilots, though the difficulties of their regional-airline partners are having a knock-on effect. United, for example, attributed some of its cuts at its former Cleveland hub last year to its regional partners' shortage of pilots.

The Government Accountability Office said in a report last year that it "found mixed evidence regarding the extent of a shortage of airline pilots."

Republic last year removed 27 of its 243 aircraft from service because of a lack of pilots. Republic Chief Executive Bryan Bedford said in an interview at the time that "the short-term answer is the aviation industry is just going to get smaller."

Republic has been unable to reach a new labor contract with its 2,200 unionized pilots since 2007. Republic said the lack of a new contract is leading more pilots to leave and is hurting its ability to attract new aviators.

Republic said it has offered its pilots compensation and work rules that would put them ahead of their peers, but the aviators rejected the proposal last year. Negotiations have been stalled since April, though talks are scheduled for this week. Republic said in the release, "due to the [pilot union's] unrealistic bargaining position, the company cannot predict with any certainty a timeline for resolution."

Republic on Friday said its second-quarter profit would be between $4 million and $5 million, or eight to 10 cents a share. Prior guidance had estimated earnings between 20 cents and 30 cents a share. Republic rescinded all previously issued financial guidance and analysts dramatically downgraded their estimates and ratings for the carrier.

Write to Jack Nicas at jack.nicas@wsj.com

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