He is also suspected of making a hoax bomb call to Delta Airlines in February 2015 which led to an emergency landing, and another against an Israeli El Al flight over Switzerland.
A statement from Israel's justice ministry said Swiss and French warplanes were scrambled to escort the El Al plane and to shoot it down if it became evident that it would crash on Swiss soil.
The teenager is also suspected of being behind a wave of threats to Jewish institutions in the US, Australia and New Zealand between January and early March.
In a statement, Victoria Police said the joint international investigation involved the FBI and police from Israel, New Zealand, United Kingdom and other law enforcement agencies.
The teenager is in custody in Israel and will be dealt with in that country's court system, on a date to be fixed.
An application by the FBI to extradite him to the US to face further charges has been refused.
FBI Director James Comey said in a Justice Department statement that the teenager's alleged behaviour, "is not a prank ... it's a federal crime".
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.
The teenager's Israeli defence lawyer has said he has autism and a brain tumour. His alleged motive is unclear.
His lawyer suggested his medical condition might have led him to wrongdoing through no fault of his own.
The teenager's arrest came after an investigation by agencies in several countries, including the Australian Federal Police and Victoria Police, and just a day after a Victorian teenager was bailed over similar hoaxes.
However, a Victoria Police spokesman said the two teenagers acted separately and their cases were not linked.