The attorney general made his position known in a recent phone call with White House counsel Donald McGahn.
The annual report is the first to reflect the Trump administration’s views and priorities.
Former law enforcement officials fear the dispute is undermining the FBI’s credibility.
The case will now be weighed by Deputy Attorney General Rod J. Rosenstein and then by Attorney General Jeff Sessions.
Trump complained to Comey that Flynn had been slow to arrange call with Russia’s leader.
The president, Comey wrote, questioned the judgment of national security adviser Michael Flynn and said Putin bragged about Russia’s prostitutes.
New policies will loosen restrictions on the export of U.S.-made drones.
It is possible the FBI’s former No. 2 official could be charged with a federal crime.
The three-judge panel said the use of the term “sanctuary cities” is an attack on local authorities.
The president lashed out on Twitter again hours after Gov. Jerry Brown said he had reached a deal with federal officials to send personnel to the Mexican border.
The state will deploy as many as 400 troops but bar them from helping border agents.
One Republican senator says the administration seems determined to give Syria to Assad, Russia and Iran.
Bipartisan legislation would initiate a five-year research project.
Three members of the Tennessee Air National Guard were punished after last week's re-enlistment ceremony.
Questions reflect growing discomfort with support for Saudi-led war against Houthi rebels.