NEW YORK — Prosecutors charged former president Donald Trump's business with a 15-year "scheme to defraud" the government and charged its chief financial officer with grand larceny and tax fraud in a Manhattan courtroom Thursday, describing what they said was a wide-ranging effort to hide income from tax authorities.

In charging papers, prosecutors alleged that the Trump Organization effectively kept two sets of books. In one — for internal use — it carefully tallied the value of benefits given to executives as part of their compensation: apartments, cars, furniture, tuition payments, even money for holiday gifts.

But in the documents that the Trump Organization sent to tax authorities, prosecutors said, those benefits were omitted. Prosecutors said the result was that the Trump Organization and its executives avoided taxes on their full compensation: CFO Allen Weisselberg, they said, avoided paying more than $900,000.

"To put it bluntly, this was a sweeping and audacious illegal payments scheme," said Carey Dunne, a prosecutor working for Manhattan District Attorney Cyrus R. Vance Jr. (D), at an arraignment hearing. He rejected an allegation from the Trump Organization that the charges were part of a politically motivated effort to hurt Trump: "It's not about politics," he said.

Dunne said the company's "former CEO" — apparently a reference to Trump — had personally signed "many of the illegal compensation checks." But Trump was not charged Thursday. The charging documents said Weisselberg orchestrated the scheme with "others" from the company but did not say who.

Weisselberg, 73, was charged with 15 felony counts including grand larceny, criminal tax fraud and falsifying business records. He pleaded not guilty during the brief arraignment hearing Thursday afternoon.

In 10 of the cases, Weisselberg was charged alongside two Trump corporate entities: Trump Corp., which prosecutors said handled executive pay, and an entity called Trump Payroll Corp. A Trump Organization attorney pleaded not guilty on their behalf.

The most serious charge against Weisselberg, grand larceny in the second degree, carries a maximum sentence of five to 15 years in prison. But none of the charges carry a mandatory prison sentence, meaning that — even if convicted on all counts — he would not necessarily face jail.

If Trump's companies were convicted, they could face hundreds of thousands of dollars in fines.

After the court hearing, attorneys for Trump derided the case as a political attack from two elected Democrats: Vance and New York Attorney General Letitia James, who had teamed up after investigating Trump's finances separately. These are the first charges to result from their investigations.

"The District Attorney is supposed to be apolitical, but everyone knows that the only reason they are proceeding with this case is because it is 'Trump,' " Trump attorney Ronald Fischetti said in a written statement. "As far as we are concerned, this case is over."

Trump, in a written statement issued shortly after the indictment, echoed Fischetti’s attack.

“The political Witch Hunt by the Radical Left Democrats, with New York now taking over the assignment, continues,” he wrote. “It is dividing our Country like never before!”

Vance and James have been investigating Trump's company since 2018, gathering millions of pages of records and subpoenaing documents from a broad array of Trump's business partners and vendors.

But while their investigation has been broad, Thursday's indictments were deep and narrow — focused only on the Trump Organization's alleged efforts to evade taxes on executive pay.

There was no mention of several other topics that prosecutors have previously said they were investigating.

Those have included hush-money payments made during the 2016 election, allegations that Trump misled lenders and taxing authorities about the values of his properties, and allegations that he did not pay proper taxes on a $102 million forgiven debt, according to previous court documents.

Prosecutors declined to comment Thursday about why those topics were not mentioned. In a written statement, James said only that "this investigation will continue, and we will follow the facts and the law wherever they may lead."

Previously, a person familiar with the investigation said prosecutors had hoped to "flip" Weisselberg, convincing him to testify against Trump in exchange for a reduction in his own charges. There has been no public indication that Weisselberg has done so. On Thursday, his attorneys Mary Mulligan and Bryan Skarlatos issued a statement saying Weisselberg "intends to fight these charges in court."

Weisselberg had surrendered at the Manhattan District Attorney's Office early Thursday, the morning after a grand jury filed indictments against him and the Trump Organization. More than five hours afterward, he walked into a courtroom for his arraignment wearing handcuffs, with detectives holding his arms. His face was flushed as the officers struggled to unlock his handcuffs.

He was released after the hearing but was required to surrender his passport after prosecutors said he was a "flight risk."

In a statement, the Trump Organization lauded Weisselberg as “a loving and devoted husband, father and grandfather who has worked at the Trump Organization for 48 years.”

“He is now being used by the Manhattan District Attorney as a pawn in a scorched earth attempt to harm the former President. The District Attorney is bringing a criminal prosecution involving employee benefits that neither the IRS nor any other District Attorney would ever think of bringing,” the statement said. “This is not justice; this is politics.”

But Dunne told New York Supreme Court Justice Juan Merchan that, counter to Trump's recent suggestion, the contents of the indictment did not detail "standard practice in the business community." The charged crimes, he added, were "not the act of a rogue or isolated employee . . . [but were] orchestrated by the most senior executives who were financially benefiting themselves and the company by getting secret pay raises at the expense of the state and federal tax payers."

The prosecutor also said the Trump Organization, "at the highest levels, decided not to accept responsibility and cooperate, which is what companies do if they want to be viewed as a good corporate citizen."

The investigation was stymied considerably by a battle waged by Trump to keep his personal and business tax returns out of the hands of prosecutors — an unsuccessful legal push that landed Trump-backed challenges at the Supreme Court twice.

"There is no clearer example of a company that should be held to criminal account," Dunne said, attempting to shoot down the Trump-backed accusation that the probe was politically motivated.

In a 25-page indictment, prosecutors said Weisselberg was at the center of a scheme that benefited at least three other unnamed Trump Organization executives, as well as Weisselberg's family members.

Dunne described it as a mechanism to provide "secret pay raises" without tax. In Weisselberg's case, prosecutors said, he was able to avoid taxes more than $1.7 million in income.

Prosecutors said the Trump Organization subsidized several areas of Weisselberg's life:

●Starting in 2005, they said, Weisselberg allegedly had the Trump Organization pay the rent and utilities for an apartment where he lived on Manhattan's Upper West Side.

●From 2005 to 2017, prosecutors said, Weisselberg also had the Trump Organization pay to lease Mercedes-Benz cars for him and his wife.

●Weisselberg also used Trump Organization funds to pay for furniture, holiday gifts and carpeting for his home in Florida, they said in court documents.

In every case, prosecutors said, the Trump Organization treated these benefits as compensation on its internal ledgers, as part of the $940,000 salary Weisselberg was supposed to be paid. But they allegedly did not report them as income to tax authorities.

The indictment said Weisselberg and other Trump executives also benefited from the payment of bonuses as if they were non-employee contractors. That allowed Weisselberg to take part in a retirement savings program for self-employed people, when he should not have, prosecutors said.

And prosecutors said Weisselberg had caused Trump to make $359,000 in private-school tuition payments for Weisselberg's grandchildren. Then, they said, in 2016 Weisselberg told an underling to delete a notation saying that the payments were made "per Allen Weisselberg" — erasing his role.

The now-merged investigations of Trump’s company by Vance and James appear to be the longest-lasting and most extensive prosecutorial examination ever undertaken of the Trump Organization.

Vance’s office opened an investigation in 2018, responding to former Trump attorney Michael Cohen’s charges that Trump had directed improper payoffs during the 2016 presidential campaign to women who said they had affairs with Trump.

But Vance’s probe then expanded, encompassing years of business transactions. Vance examined tax breaks that Trump got on an estate in suburban New York, loans Trump took out on his Chicago tower and statements Trump made to New York tax authorities about the value of his Manhattan towers, according to previous court filings.

Vance did not seek reelection this year; that means the bulk of the case against Trump’s company could be handled by his successor.

Trump and his organization have never faced criminal charges, but the former president has been the target of lawsuits from the office of the New York attorney general.

In one, he was sued on allegations he defrauded students at Trump University, a case that ended with Trump paying a $25 million settlement in 2016 in that and other cases. Two years later, Trump was sued for misusing money in a charity he controlled; a judge ordered him to pay damages of $2 million.

An earlier version of this article misspelled Letitia James’s first name as Leticia. The article has been corrected.