The president, accompanied by the First Lady Iriana Joko Widodo, and boarded the Indonesian-1 presidential plane, which took off from Singapore`s Changi Airport, at 06:50 local time.
The presidential delegation directly headed to Merauke in Papua to conduct a working visit on Friday.
Jokowi would then make a working visit to Papua New Guinea (PNG) to attend the 2018 APEC Summit on Nov 17, 2018.
Earlier, the president attended the 33rd ASEAN Summit and other summits for three days from Tuesday (Nov 13).
Jokowi arrived in Singapore on Tuesday afternoon for the ASEAN Summit.
Reporting by Bayu Prasetyo
Editing by Bustanudin