The companies' land was cordoned off by the police and the firms can face charges, Environment Ministry spokesperson Djati Witjaksono Hadi told Efe news.
Among the companies under investigation are four subsidiaries of Malaysian firms and a Singaporean entity that manages palm oil plantations, a sector which contributes to deforestation in Indonesia.
The spokesperson did not provide further details about the companies, nor charges that can be filed against them.
The Indonesian fires, which began at the beginning of the dry season in June and worsened at the beginning of September, have caused environmental, health and diplomatic crises as the haze has spread to neighbouring Malaysia and Singapore.
The clouds of smoke have caused the delay and cancellation of hundreds of flights in September, as well as the closure of schools on Sumatra and Borneo.
The situation has also worsened air quality in Singapore and Malaysia where the governments have asked Indonesia to take action on the matter.
More than 9,000 firefighting personnel and other Indonesian agencies are battling the fires, which are particularly severe in central and northern Sumatra along with central and western Borneo, where Malaysian and Indonesian authorities are trying to create artificial rain through cloud seeding.
Indonesian authorities estimated that up until August, around 320,000 hectares were burnt and 39 per cent of the current hotspots are in peat bogs, which have carbon-rich soil. When burned, these have a big impact through CO2 emissions.
( With inputs from IANS )