A courthouse staffer secretly pocketed $160,000 in fines that New Yorkers mailed in for low-level offenses — leading to the wrongful arrests of at least five people, authorities said Tuesday.

Carlos Sanchez, 36, allegedly swiped more than 500 money orders and cashier’s checks intended to pay fines for low-level offenses like public urination and public consumption of alcohol, prosecutors charge.

“This court employee is accused of lining his pockets with payments submitted by hundreds of New Yorkers striving to resolve their criminal summons cases lawfully and responsibly,” said Manhattan District Attorney Cy Vance Jr. in a statement.

“While his scheme cost the New York court system more than $160,000, the human costs of his conduct were much greater.”

Bench warrants were issued for at least 15 defendants and at least five were arrested and detained for fines they thought they paid, officials said.

At least six companies, who had paid fines for building and fire code violations, had judgments issued against them for nonpayment while at least one paid the fine twice, according to the DA’s office.

Some businesses that made timely payments were even hounded by collection agencies.

Sanchez was hauled out of 1 Centre St in cuffs Tuesday morning and taken to Manhattan Supreme Court, where he was arraigned on 46 counts of grand larceny, possession of a forged instrument and falsifying business records.

“Not guilty,” mumbled Sanchez before Justice Daniel FitzGerald.

As a senior court office assistant, Sanchez was tasked with opening and sorting summons payments, said Assistant District Attorney Robert Cannata, successfully arguing for $25,000 bail.

For more than a year starting in Jan. 2015, Sanchez allegedly doctored the checks and money orders then deposited them into his personal bank accounts or used them to pay his credit card bills, the prosecutor said.

Prosecutors are seeking state prison time for the “egregious conduct,” Cannata said.

He added that the disgraced court staffer had wired $40,000 of his illicit profits to two women in Colombia and one in Germany, making him a flight risk.

Defense lawyer Verena Powell said Sanchez has no criminal record and “maintains his innocence.”