Indonesian aviation officials were unhappy over the decision, saying the ban was ill-informed as it failed to take into account recent improvements to airline safety.
The EU "blacklist" is updated every three months based on reports from the US Federal Aviation Administration and the International Civil Aviation Organisation (ICAO), as well as reports from individual countries.
Jean Breteche, the EU's ambassador to Indonesia, said the EU team would check with the affected airlines on their safety conditions.
"We hope to reverse the decision as soon as possible ... if the EU has enough proof of safety conditions," he said after a meeting with Indonesian aviation officials.
Indonesia's air safety record has come under scrutiny after two major accidents this year.
In March, a Garuda passenger jet with 140 people on board overshot the runway in Yogyakarta in Java and burst into flames, killing 21 people.
In January, an aircraft belonging to budget carrier Adam Air crashed into the sea off Sulawesi, and has yet to be found. All 102 people on board are presumed dead.
Indonesia signed an agreement last week with ICAO to improve air safety by committing to implement safety management based on international standards.
Indonesia also started issuing safety rankings following the Garuda crash in March. Garuda made the top of three levels in the latest rankings issued last month.
Air travel in Indonesia grew into a booming industry following the liberalisation of the aviation sector in 1999, but the rapid growth raised questions over whether safety has been compromised.