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A Boston charity headed by Suffolk Construction chief executive John Fish is acknowledging that it made an error in donating $250,000 to a political action committee supporting Hillary Clinton’s presidential campaign.

Suffolk Cares Inc., which lists Fish as its president, gave the money in two separate donations in September and October to Correct the Record, a super PAC backing the Democratic nominee. Federal tax rules prohibit charities organized as 501(c)(3) nonprofits such as Suffolk Cares from making political donations.

In a statement, Suffolk Construction spokesman Daniel Antonellis described the donations as an “accounting error.”

“Once Suffolk Cares discovered this accounting error, the funds were immediately returned,” he said.

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Antonellis declined to comment further.

Representatives from Correct the Record did not respond to requests for comment Tuesday. But a spokeswoman told the Center for Public Integrity, which first reported the donations, that the group had returned the money upon learning of the violation.

“Contributions to political campaign funds or public statements of position (verbal or written) made on behalf of the organization in favor of or in opposition to any candidate for public office clearly violate the prohibition against political campaign activity,” the Internal Revenue Service says on its website.

The IRS declined to comment, citing rules against discussing specific cases.

Lloyd Hitoshi Mayer, a professor at Notre Dame University who studies nonprofit tax law, said the officers of Suffolk Cares should have known the donations were improper.

“At a minimum, it is a pretty egregious internal controls mistake,” he said. “Because all you had to do was Google it.”

Mayer said the IRS could penalize Suffolk 10 percent of the donations, which would be $25,000. This year, Republican presidential nominee Donald Trump’s charitable foundation paid a similar penalty for donating to a political committee supporting the reelection of Florida Attorney General Pam Bondi. At the time of the donation, Bondi was reportedly considering whether to join with other states in investigating a Trump business venture.

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Suffolk Cares distributed more than $12 million in grants and gifts in the fiscal year that ended Aug. 31, 2015, the most recent year for which records are available.

Fish was also the largest source of money for Suffolk Cares charitable giving; he reported donating $12.3 million to Suffolk Cares in the fiscal year that ended Aug. 31, 2015, while privately held Suffolk Construction donated another $1.3 million.

Recipients included local schools such as Boston College and Emerson College, health care organizations, the city of Boston Scholarship fund, a summer camp for inner-city kids, the Boys & Girls Clubs of Boston, and dozens other charities and nonprofits.

The foundation donated $1 million to Boston 2024, the doomed Olympic organizing group that Fish led. And it donated to charities associated with Mayor Martin J. Walsh and City Councilor Tito Jackson.

Also that year, Suffolk Cares gave $100,000 to the Bill, Hillary, and Chelsea Clinton Foundation, the charity whose operations have faced scrutiny throughout the election and during Clinton’s tenure as secretary of state.

In July, the Campaign Legal Center, a political finance watchdog, filed a complaint with the Federal Election Commission alleging Fish’s company, Suffolk Construction, improperly donated $200,000 to another pro-Clinton super PAC, Priorities USA. The Campaign Legal Center said Suffolk Construction is prohibited from making donations to federal political committees because it is a contractor to the US government.

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“It certainly appears that Suffolk is looking at every avenue to put money into this election,” said Brendan Fischer, an attorney with the Campaign Legal Center, in response to the new charitable donation.

Priorities USA returned the $200,000 to Suffolk Construction in June, according to campaign finance reports.

Fish has personally donated this election cycle across the political spectrum, according to the Federal Election Commission. He has given to Clinton, her former Democratic opponent Martin O’Malley, former Republican candidates Marco Rubio and Chris Christie, and Libertarian candidate Gary Johnson.


Adam Vaccaro can be reached at adam.vaccaro@globe.com. Follow him on Twitter at @adamtvaccaro.