The decision to deny the flight of Israeli Prime Minister Benjamin Netanyahu from flying over Indonesian airspace was intended as retaliation against Israel's action last year, which banned the foreign minister of Indonesia from visiting Palestine.
Indonesia's foreign ministry confirmed today that the decision was taken because Israel did 'the same' to Indonesia, reported Anadolu news agency.
On Wednesday, Israeli Prime Minister Benjamin Netanyahu's plane had to make a detour en route from Singapore to Australia after it was banned from using Indonesian airspace.
The plane arrived in Sydney after an 11-hour flight from Singapore even though the normal time for a direct flight between the two locations is eight-and-a-half hours.
Indonesia is the world's most populous Muslim country with a total population of about 240 million. The country strongly supports Palestinian aspirations for independence.
Foreign ministry spokesman Armanatha Nasir said: "This occurrence is normal and no cause for concern" since Indonesia and Israel do not have diplomatic relations.
Nasir, quoted by detik.com, added: "[This decision was taken] because the same was done to us."
In March 2016, the Indonesian foreign minister was set to inaugurate the Honorary Consul of Indonesia in Ramallah. However, Tel Aviv did not give him permission to fly to Palestine moments before the minister's departure.