The decision came despite Manning pleaded guilty to 10 lesser charges that carry a maximum total sentence of 20 years, The New York Times reported Friday.
Manning admitted in court Thursday that he had furnished WikiLeaks with about 700,000 government documents.
However, he pleaded not guilty to the more serious charges of aiding the enemy, violating the Espionage Act and the Computer Fraud and Abuse Act, larceny and the improper use of government information systems.
The decision by prosecutors means the military will proceed with plans to begin Manning's' court-martial on June 3, during which 141 witnesses are scheduled to testify for the prosecution.
Reading a 35-page statement during his plea, Manning said he had leaked the material to "spark a debate about foreign policy."
The government has said some of the documents Manning released ended up in the hands of Osama bin Laden.