FIFA president Gianni Infantino announced Friday that Indonesia had been reinstated after Jakarta sent a letter notifying that it had lifted sanctions on national football body, the PSSI.
Indonesia has been without a national football competition for the better part of a year, after a feud between the PSSI and its sports ministry saw the top-grade tournament suspended.
"We hope the lifting of the ban will push the nation to improve its national football, especially in regards to revamping its organisational management, increasing transparency, accountability and enhancing a more harmonious relationship with the various stakeholders," Indonesia's sports ministry said in a statement.
Asian Football Confederation president Sheikh Salman bin Ebrahim Al Khalifa also applauded the move.
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"We welcome them (Indonesia) back into the Asian football family," he said in a statement.
"However, the AFC executive committee reiterated this week their continued stand against government intervention in sport generally and football in particular."
AFC officials will meet their Indonesian counterparts to discuss next steps regarding competition matters, the statement said.
Indonesia launched an interim eight-month competition in April, but the sports ministry said this was not a replacement for its top-flight league.