The shooting at three vehicles trying to enter the airport happened "in a particularly confusing situation", just as French troops had been fired upon "from an unknown source," it said.
Another Indian and a Chadian were injured in the shooting.
"These vehicles were transporting Chadian and Indian nationals. Despite warning shots fired by troops guarding the site, the vehicles kept going at high speed," the ministry said in a statement.
"Two Indian nationals died. French forces immediately took charge of the injured Indian and the Chadian, who were driven to an aid facility."
Around 300 French soldiers were dispatched to the Central African Republic over the weekend to reinforce troops already present in the capital Bangui, which was seized by rebels on Sunday.
The United Nations has since called emergency talks after the bloody coup sent ousted leader Francois Bozize fleeing across the border.
The defence ministry said it "shares the pain of the families and sends them -- as well as Indian authorities -- its sincere condolences", adding it had ordered a probe into the incident.
"The president has sent a message of solidarity to the Indian prime minister. Defence Minister Jean-Yves Le Drian is due to hold discussions with his Indian counterpart in the next few hours."