The travel time from Yogyakarta will take around 68 minutes, while the Prameks will need an average time of 75 minutes after seven stops.
state-owned train operator PT KAI Commuter would limit the number of passengers in following health protocols.
Jokowi also underscored the importance of using eco-friendly mass transportation in the future.
"This is an eco-friendly mode of mass transportation. I was informed that the commuter line is 10 minutes faster than Prameks," he said at Yogyakarta Tugu Station.
Discourse on extending the route to Madiun
The Ministry of Transportation plans to extend the routes from Yogyakarta and Solo in Central Java to Madiun in East Java.
The ministry's spokesperson Adita Irawati said that the number of commuter line services will be increased in the future.
"It will be extended not only from Yogyakarta to the north side of the city but also to the east side. It's certainly part of a long-term plan," said Aditia at Klaten Station in Central Java.