The US Federal Aviation Administration (FAA) ordered three US carriers that fly to Israel – Delta, United and US Airways – to halt flights for 24 hours.
European carriers Lufthansa, KLM, and Air France have also cancelled flights to Tel Aviv.
The move comes amid heightened scrutiny over flights near conflict zones.
Israel’s Transportation Ministry asked the airlines to reverse their decision, saying the airport was “safe for landings and departures”.
“Ben Gurion Airport is safe and completely guarded and there is no reason whatsoever that American companies would stop their flights and hand terror a prize,” it said in a statement.
The FAA’s prohibition only applies to US airlines. The agency has no authority over foreign airlines operating to or from the airport.
However, Lufthansa – which includes Swiss, Germanwings and Austrian Airlines – said it had decided to suspend flights to Israel for two days.
Air France and KLM also said they had suspended flights scheduled to depart on Tuesday.
However, Air France said a flight scheduled for Wednesday is still scheduled to depart.
Delta said a flight from New York City to Tel Aviv was diverted to Paris on Tuesday after Israeli police confirmed that a rocket landed approximately one mile from Ben Gurion airport.
Both and United said they had suspended operations in Israel for the near future – beyond the FAA’s 24-hr period.
US Airways said it had not yet made a decision.
British Airways wrote on Twitter: “We are closely monitoring the situation. Our flights are currently operating as scheduled.”
The halt in service comes less than a week after Israel began a ground operation in Gaza, and as airlines around the world re-think their flight paths over conflict areas in the wake of the crash of Malaysia Airlines flight MH17 in eastern Ukraine.
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