The development has been widely expected ever since Snowden revealed his identity by video nearly two weeks ago.
Filing a criminal complaint is also the first step in the process the government would undertake to have Snowden extradited from Hong Kong, where he is believed to be hiding.
In an interview with Charlie Rose this week, President Obama hinted at that outcome.
“The case has been referred to the DOJ for criminal investigation … and possible extradition," he said. "I will leave it up to them to answer those questions.”