Washington (CNN) - Defense Secretary Robert Gates has "real reservations" about the top U.S. intelligence officer in Afghanistan publishing his recommendations for improved intelligence operations in that country, according to a Pentagon spokesman.
Maj. Gen, Michael Flynn, deputy chief of staff for intelligence in Afghanistan, published a nearly 30-page document entitled "Fixing Intel: A Blueprint for Making Intelligence Relevant in Afghanistan," through the Center for a New American Security (CNAS), a Washington, D.C.-based think tank. The center is closely affiliated with the Obama administration and with experts consulted by Democratic officials.
The report was deeply critical of ongoing intelligence activities and made several recommendations for changes.
Publication through a think tank was highly unorthodox, especially for an intelligence-related matter.
Geoff Morrell, the Pentagon press secretary, said Thursday that Gates thought the analysis by Flynn was "brilliant" and the recommendations were "spot on."
But "that said, he (Gates) has real reservations about the general's choice of venue for publication," Morrell said.
The Pentagon was trying to still determine if the report underwent a security review to see if any classified material was disclosed, according to a senior Defense Department official.
The official declined to speak on the record because he said the secretary was "addressing" the matter of how the report came to be privately published.
He said he did not know if Flynn was going to be reprimanded. He also said it was not clear if Gen. Stanley McChrystal, the commander of U.S. forces in Afghanistan, knew about the report before it was published.
The official also said that Michelle Flournoy, the number-three ranking official at the Pentagon who used to work at CNAS, was not aware of her former employer was publishing the report.