The case was revealed in a court document known as a "criminal information" that the Justice Department said it filed to stop the 10-year statute of limitations on the offence from expiring earlier this month.
The document filed in Washington federal court charges Comey with transmitting and conspiring to transmit national defence information. It alleges he shared classified information with a reporter from the New York Times in October 2016.
Comey said in a video on Instagram that "they're back again" and referenced the Justice Department, but did not provide further details.
"I'm still innocent," he added.
The Trump administration is employing the unusual manoeuvre of bypassing a grand jury - a move Comey's lawyers say makes the case legally invalid.
Comey's lawyers have already asked a judge to dismiss the case.
The new case adds to the legal fights facing Comey, whom the Justice Department has already charged twice, accusing him of lying to Congress about media leaks and threatening President Donald Trump in a social media post.
A judge dismissed the false statements case, while the threats case remains pending.
Comey's lawyer, Patrick Fitzgerald, said in a statement that the document "purports to charge Mr Comey with crimes that he did not commit".
The criminal information was filed on October 5, but was unsealed on Monday at the request of Comey's lawyers.
A Justice Department spokesperson described the manoeuvre to halt the statute of limitations as a "widely recognised practise in federal court".
"This is an ongoing criminal investigation, and we will not comment further," the spokesperson said in a statement.
