The province is accusing Cargill Limited of failing to immediately report a case where samples from the company's High River plant's industrial waste water system were allegedly falsified.
The government is also charging a man who no longer works at Cargill in connection with the April 2012 allegations.
The charges under Alberta's Environmental Protection and Enhancement Act could result in fines or other penalties.
Cargill says the test results were compromised during a time when its waste water treatment system was being improved.
The company says it conducted its own internal investigation and reported its finding to Alberta officials.
"Following the report, Cargill implemented the necessary corrective actions that would have the facility back into compliance with regulations," Cargill said in a statement from Winnipeg
"Throughout this process Cargill co-operated fully with government officials."
Cargill and Pushp Pal Singh of Calgary are to appear in Okotoks provincial court on the charges May 27.
Alberta Environment officials declined comment.