The world's fourth most populous country grappled with a devastating second wave of infections in July, driven by the spread of the Delta variant.
Daily case numbers dropped to around 200 by December, before rising this month amid reports of local transmission of the Omicron variant.
"Local transmission has been found and Jakarta has become an infection cluster," Health Minister Budi Gunadi Sadikin said in a statement on Saturday. "We need to coordinate with regional government to tighten mobility and strengthen health protocols, (give) booster vaccine shots and strengthen health facilities."
He did not elaborate on what restrictions local authorities might impose. Officials usually review pandemic-related measures each Monday.
Indonesia detected its first COVID-19 case of the more contagious Omicron variant on Dec. 16. Confirmed case numbers have reached more than 500 since then and officials have said infection rates could peak in February.
The southeast Asian nation started its vaccine booster programme for the general public this week.
(Reporting by Bernadette Christina Munthe; Writing by Gayatri Suroyo; Editing by Mike Harrison)