Adani admitted in December that its Carmichael proposal would lead to "unavoidable vegetation clearing" on land where endangered black-throated finches live.
But Greenpeace Australia research co-ordinator Georgina Woods says the company has failed to outline its poor environmental record in India.
The activist group argues Adani has tried to destroy tiger habitats and flood villages as part of power generation expansion plans.
Mr Burke has asked his department to investigate the claims as Adani seeks to operate the $6.1 billion Carmichael coal and rail project at Clermont from 2015.
"These are serious allegations that need to be checked," he told AAP in a statement.
"Every company needs to know that cutting corners on the assessment process will get you nowhere.
Public consultations on Adani's environmental impact statement closed this week.
Comment has been sought from Adani.
Adani later told AAP it would work with government to address submissions received during the public consultation process.
"Adani is aware of its responsibilities under state and commonwealth legislation and ensures its operations meet those requirements," the company said in a statement on Wednesday.