Justice Department spokesman Brian Fallon declined comment Saturday on the new development beyond the court filing.
The program at issue in the Muhtorov case is commonly called "702," a reference to the numbered section of the surveillance law on Internet communication.
In the Muhtorov case, after his contact with the IJU's website administrator, the FBI went to court and obtained email from two accounts that Muhtorov used, according to the court papers.
The FBI also went to court to obtain communications originating from Muhtorov's phone lines. In one call, Muhtorov told an associate that the Islamic Jihad Union said it needed support, an FBI agent said in an affidavit filed in the case. The associate warned Muhtorov to be careful about talking about a founder of group, the affidavit stated.
The FBI also said Muhtorov communicated with a contact in the group by email using code words, telling a contact that he was "ready for any task, even with the risk of dying."
Muhtorov, a refugee from Uzbekistan, resettled in Aurora, Colo., in 2007 with the help of the United Nations and the U.S. government. He was arrested Jan. 21, 2012, in Chicago with about $2,800 in cash, two shrink-wrapped iPhones and an iPad as well as a GPS device.
In March 2012, Muhtorov's attorney, federal public defender Brian Leedy, said at a court hearing that Muhtorov denied the allegations and had been headed to the Uzbekistan region to visit family, including a sister who remains imprisoned in that country.
The IJU first conducted attacks in 2004, targeting a bazaar and police, and killing 47 people, according to court papers in the case. The organization subsequently carried out suicide bombings of the U.S. and Israeli embassies and the Uzbekistani prosecutor general's office in Tashkent, Uzbekistan, the court papers stated.
Before the recent leak of U.S. documents showing widespread government surveillance, dozens of consumer suits were filed against the government and telecommunications companies over obtaining customer data without warrants. Nearly all the cases were tossed out when Congress in 2008 granted the telecommunication companies retroactive immunity from legal challenges.