The civil suit was filed Wednesday in a Jakarta court against PTTEP Australasia, which was operating the rig in the Timor Sea where the accident happened, and its parent company, Thailand's state-owned PTT Exploration and Production.
The spill in the Montara field, north of Australia, took place in August 2009. Thousands of barrels of oil leaked for close to 10 weeks following a blowout at the rig, in Australia's worst ever offshore drilling accident.
Indonesia is seeking about 27.4 trillion rupiah (around $2 billion) in damages, including for damage caused to the environment, after the oil spread into its waters, said Arif Havas Oegroseno, deputy minister for maritime affairs.
The government is also seeking to freeze the firm's assets in Indonesia and overseas, he said.
"This is an effort to seek justice for the PTTEP oil spill," Oegroseno said.
Oegroseno said the oil spill killed and damaged a huge area of coral reefs, seagrass meadows and mangroves in Indonesia.
Over the years, Indonesia had tried to negotiate with the company to come to a resolution but was not satisfied with their response, Oegroseno said.
"We feel that they are not serious in handling this issue," he said.
An independent commission which included the former Indonesian and Thailand foreign ministers did not manage to resolve the issue when PTTEP failed to show up for the signing of an agreement over the oil spill in late 2012, the deputy minister said.
Oegroseno said the company's failure to show up was a "clear signal" that the company was not taking the case seriously.
There was no immediate comment from the energy company.
PTTEP has previously said comprehensive studies clearly showed "no lasting impact on the highly sensitive and biodiverse ecosystems in the areas closest to Indonesian waters".
In August last year about 13,000 Indonesian seaweed farmers launched a AUS$200 million class action against PTTEP Australasia in Sydney, claiming the accident devastated their livelihoods.
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