Police said the suspect was 19, but gave no further identifying details.
Police spokeswoman Luba Samri said the suspect was "a resident of the south (of Israel) from the Jewish community".
Police said the suspect was 19, but gave no further identifying details. Israeli media said he was a dual Israeli-US national.
"The investigation began in several countries at the same time, in which dozens of threatening calls were received at public places, events, synagogues and community buildings that caused panic and disrupted events and activities in various organisations," a police statement said.
It said that the investigation was undertaken in cooperation with the FBI "as well as other police organisations from various countries."
Israeli authorities did not directly link the arrest with a wave of more than 100 bomb threats against US Jewish organisations since the beginning of the year.
"We hope that this investigation will help shed light on some of the recent threats against Jewish institutions, which have caused great concern both among Jewish communities and the Israeli government," Israeli public security minister Gilad Erdan said in a statement.