A plane from Israel was about to land at the airport, which had been informed and went to the airport to look for the passengers.
"After unknown persons entered the traffic zone at Makhachkala airport, a decision has been made to temporarily close the airport to arriving and departing flights," the Russian Civil Aviation Authority said in a statement.
Israel is now calling on Russian authorities to protect Israeli citizens and Jews in the country.
"The State of Israel takes seriously all attempts to harm Israeli citizens and Jews wherever they are," it said in a statement, according to the Reuters news agency.
All planes that were on their way to the airport have been diverted, according to the Russian Civil Aviation Authority.