Justice Juan Merchan in Manhattan also said jury selection for the trial of the Trump Organization and its former Chief Financial Officer Allen Weisselberg will begin on Oct. 24, 15 days before the Nov. 8 midterm elections.
Donald Trump is not among the defendants.
The judge rejected arguments by Trump's New York City-based company and Weisselberg that they had been selectively prosecuted, and that federal courts were better positioned to determine whether the Internal Revenue Service had been defrauded, among other bids to dismiss charges.
The judge did toss one charge from the 15-count indictment against the Trump Organization because it had been brought too late.
Hearings on other motions are scheduled for September.
In the indictment, the Trump Organization and Weisselberg are accused of having defrauded tax authorities over 15 years by awarding "off-the-books" benefits to company executives.
Weisselberg was charged with evading $1.7 million of income, including rent for a Manhattan apartment, lease payments for two Mercedes-Benz vehicles and tuition for family members, with Trump signing checks for the tuition himself.
Other charges in the indictment include scheming to defraud, tax fraud and falsifying business records.
The defendants have pleaded not guilty. The Trump Organization could face fines and other penalties. Weisselberg is also charged with grand larceny, which carries a maximum 15-year prison term on conviction.
The charges arose from an investigation by former Manhattan District Attorney Cyrus Vance. Vance's probe into Donald Trump's activities appeared to lose steam after Alvin Bragg succeeded him as district attorney in January.
Two prosecutors who had been leading the probe resigned in February, and one, Mark Pomerantz, has said he believed felony charges should be brought against the Republican former president but that Bragg indicated he had doubts.
Bragg's office has said the investigation is continuing.
Friday's hearing came as the United States is asking a federal judge in Florida to unseal a search warrant executed on Monday at Trump's Florida residence, along with a redacted list of the items retrieved by FBI agents.
Separately, Trump spent several hours on Wednesday in a deposition for New York Attorney General Letitia James' civil probe into his business practices.
Trump refused to answer questions, invoking his Fifth Amendment constitutional right against self-incrimination.
(Reporting by Karen Freifeld in New York; editing by Jonathan Oatis)
By Karen Freifeld and Jonathan Stempel