The lost suitcase -- with weapons inside -- was eventually discovered in Los Angeles. Four Glock 9 mm handguns that were in the bag are now missing and police officials say they believe they were stolen.
The bag was supposed to have been on the flight from JFK to Washington DC where additional Israeli security officers were being assigned to help with the Israeli leader's visit with President Obama at the White House.
Port Authority police at JFK are now investigating whether the guns were stolen in New York or after the errant bag arrived in Los Angeles, a PA spokesman said.
Officials said security protocols require travelers with handguns to pack the weapons and send them via checked luggage.
One source said the bag was inspected by Transportation Security Administration screeners who put a seal over the bag at Kennedy Airport, clearing the weapons for shipment to Washington.
A spokesman for the Israeli Consulate referred all calls about the lost bag and the missing handguns to American Airlines.
"When you have a situation related to security, we allow the appropriate law enforcement agencies to handle the situation and we refrain from commenting publicly, so that we don't hamper an investigation," said Tim Wagner, a spokesman for American Airlines.