Indonesia has reportedly accused FIFA of violating the country's sovereignty after world football's governing body threatened sanctions against Jakarta over government interference in its domestic league.

The row erupted when the country's football association halted the Indonesian Super League at the weekend after a dispute with an agency of the national sports ministry.

The agency, BOPI, insisted that two clubs not be allowed to participate due to ownership issues.

However, the local football association, the PSSI, insisted they be allowed to play and suspended the league when BOPI stood its ground.

In a letter to the sports ministry last week, when the dispute was simmering but before the league's suspension, FIFA Secretary General Jerome Valcke told the Indonesian government to allow the PSSI to manage its affairs independently.

Valcke warned of "possible sanctions" if Jakarta did not comply.

But the ministry at the weekend dismissed FIFA's statement as "completely wrong", and BOPI has since also added its voice to the growing anger.

"We think that FIFA has violated Indonesia's sovereignty," said a statement from the agency, cited by Kompas newspaper late Sunday.

"It is only right that FIFA understand that besides FIFA's regulations, there are laws that must be complied with by any party involved in national football."

Indonesian football has been repeatedly beset by crises, and this is not the first time that FIFA has intervened.

The governing body previously threatened to ban Indonesia from world soccer over a row between the PSSI and a breakaway association, with both sides running separate leagues. The two sides eventually agreed to come together, avoiding a ban.

Weak management, corruption, poor security at games, and high-profile cases of foreign players dying after going unpaid have also cast a shadow over football in the world's fourth most populous country.