The three suspects - who were due to appear before a US court on Thursday - include the assistant to a Coca Cola executive who is alleged to have stolen documents and a sample of a new drink.
The investigation was launched after Pepsi informed Coke about a letter it had received from a person identifying himself as "Dirk", claiming to be a high-level Coca-Cola employee, offering "very detailed and confidential information".
Pepsi spokesman Dave DeCecco said his company was happy to co-operate with Coke and the authorities.
"Competition can sometimes be fierce, but also must be fair and legal," he said.
The authorities say the FBI launched an operation to entrap the suspects.
An FBI undercover agent met one of the suspects who was posing as "Dirk" at an airport in Atlanta, Georgia, the authorities say.
The suspect gave the agent "a brown Armani Exchange bag containing one manila envelope with documents marked 'highly confidential' and one glass bottle with a white label containing a liquid product sample", a US justice department statement said.
The undercover agent paid "Dirk" $30,000 for the sample and then agreed to pay $1.5 million for the rest of the information.
The three were arrested in Atlanta on Wednesday.