Sniffer dogs are checking cargo and luggage, random checks are being carried out on cars entering airports, and screening of workers will be tightened under the heightened security measures which came into force Tuesday, the ministry said.
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"The move has been taken after recent terror attacks, and threats in several countries," ministry spokesperson JA Barata said in a statement.
Barata also said that a Jakarta airport had received a threat in recent days. However, he declined to say which of the two airports serving the capital had been targeted or to give details about the threat.
Elite anti-terror police and military personnel had already been deployed to the main airport serving Jakarta as a security measure after the Paris attacks.
Terrorists killed 130 people in Paris on November 13 in simultaneous attacks, while a Russian plane went down last month in Egypt, killing all 224 people on board, with the Islamic State group saying it bombed the airliner.
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In recent days, a Turkish Airlines plane, and two Air France planes -- all flying from the US -- were diverted due to bomb scares, but no explosives were found on the flights.
Indonesia, the world's most populous Muslim-majority country, suffered several major bomb attacks conducted by terrorists between 2000 and 2009, but a crackdown has weakened the most dangerous extremist networks.
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