Company spokeswoman Kate Shannon said the facility in Saint John faces two charges under the federal Migratory Birds Convention Act that prevent anyone from depositing a substance harmful to migratory birds. Canaport also faces a charge under the federal Species at Risk Act, Shannon said.
She said Canaport learned of the charges last week and a court appearance is set for Jan. 21 in provincial court.
"We've co-operated with the authorities throughout the investigation process and complied with all the requests for information," she said.
"We will respond to the charges in due course once we've had a chance to review the details."
Environment Canada launched an investigation after about 7,500 migrating birds were killed in September 2013 while the company was burning off excess gas at the facility.
Shannon said changes to equipment to reduce the amount of flaring have since been completed and there have been no further incidents.