A judge had dismissed the case against PT Bumi Mekar Hijau (BMH), saying there was not enough evidence that the firm failed to prevent recurring fires.
Haze from forest fires in Indonesia affected South East Asia for months.
BMH supplies Asia Pulp and Paper, one of the world's biggest such companies.
The $565m in damages from the lawsuit would have been the largest financial reward ever levied against such a firm.
The government alleges BMH failed to prevent recurring fires in 2014 and this year on about 20,000 hectares of land in a region of Sumatra.
But presiding judge Parlas Nababan in a South Sumatra court said: "The lawsuit against PT Bumi Mekar Hijau is rejected because the evidence is not proven."
The director of law enforcement at the ministry of environment, Rasio Ridho Sani told the BBC the government is looking into its legal options now and companies must be held responsible for the fires in their areas even if they were not caused directly by the firm.
The forest and peatland fires, which caused dangerous levels of pollution in large parts of South East Asia in the second half of the year, were largely located on the islands of Sumatra and Borneo.
The Indonesian government has said it will appeal against a court decision that rejected a $565m (£381m) lawsuit against a plantation company accused of causing forest fires.