The Washington Times reported that the indictment charged Franklin passed information, including a top-secret document on possible Iranian-backed insurgent attacks on U.S. forces in Iraq, to the lobbying group. That group was previously identified as the American Israeli Public Affairs Committee.
Two employees of AIPAC have been tied to the investigation and have left the organization, the Times said.
The indictment alleged that Franklin supplied data that could be used "to the injury of the United States and to the advantage of a foreign nation," the Times said.
The newspaper said the investigation of Franklin began more than three years ago.