The indictment, unveiled by Manhattan District Attorney Cy Vance, charges Manafort with 16 counts related to mortgage fraud, conspiracy and falsifying business records.
"No one is beyond the law in New York," Vance said in a statement. Manafort's alleged actions "strike at the heart of New York's sovereign interests, including the integrity of our residential mortgage market," Vance added.
Crucially, Trump does not have pardon power for state charges.
The president has not explicitly ruled out pardoning his former campaign official. But Trump has lambasted special counsel Robert Mueller's Russia probe as a "witch hunt," and in recent days has appeared to criticize investigations in New York related to his business empire.
White House spokeswoman Sarah Huckabee Sanders said Monday that the president would decide whether to pardon Manafort "when he's ready."
But Trump, when asked about whether he planned to pardon Manafort, told reporters at the White House on Wednesday afternoon that he has "not even given it a thought as of this moment."
Earlier Wednesday, a federal judge sentenced Manafort, who is 69 years old, to 43 months of additional prison time on conspiracy charges lodged by Mueller as part of his probe of Russian election meddling and possible Trump campaign collusion.
Less than a week earlier, Manafort had received a 47-month prison sentence in another federal case lodged by Mueller. Manafort's combined prison time in the Mueller cases totals 7½ years.
A spokesman for Manafort did not immediately respond to CNBC's request for comment on the state prosecutors' charges.
Manafort's charges in Mueller's cases largely related to consulting work he did for a pro-Russia political party in Ukraine years before joining Trump's presidential campaign. But the New York charges involve Manafort's conduct between 2015 and 2017, according to the indictment.