FBI Director James Comey said in a Justice Department statement that the behavior allegedly perpetrated by the suspect, Michael Ron David Kadar, "is not a prank... it's a federal crime."
Kadar was arrested in southern Israel on March 23 after a joint probe by Israeli police and the FBI.
While the US and Israel have an extradition treaty, the Justice Department statement made no mention of any effort to extradite Kadar to face the charges in a US court.
A Justice Department spokesman declined to comment further to AFP beyond what the statement said.
Kadar is suspected of being behind a wave of threats to Jewish institutions in the US, Australia and New Zealand between January and early March.
The threats -- telephoned in using software to disguise the voice and number of the caller -- typically said an assailant had planted a bomb or was armed with guns and intended to kill dozens of people, often children.
When police scrambled to the premises, which were evacuated, they found the calls to be hoaxes.
"These threats of violence instilled terror in Jewish and other communities across this country and our investigation into these acts as possible hate crimes continues," US Attorney General Jeff Sessions said in the statement.
Kadar was charged with making threatening calls to Jewish community centers in Florida, conveying false information to police dispatch in Georgia, and cyberstalking, the Justice Department said.
An acting US attorney for Florida's Middle District, Stephen Muldrow said: "The charges brought today demonstrate our resolve to pursue and prosecute those who seek to sow terror and fear in our community, wherever they may hide."
A court in Israel last Thursday extended to next Monday the detention of Kadar, whose name is subject to a gag order in that country.
His Israeli defense lawyer has said Kadar has autism and a brain tumor.
Kadar's alleged motive is unclear. His lawyer suggested his medical condition might have led him to wrongdoing through no fault of his own.
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