Gration resigned after seeing a draft of the report, the officials said.
Three U.S. Embassy employees told the Associated Press that Gration led the embassy using a "my way or the highway" military leadership style that didn't translate well in the civilian embassy world. The employees asked not to be identified, fearing retribution.
The U.S. Embassy statement announcing Gration's departure laid bare the disagreements the former military leader had with his civilian bosses at the State Department and other U.S. agencies. Gration said being ambassador to Kenya was "a dream job."
"It has been a great honor and a profound privilege to be a part of the U.S. State Department team for the past three years and to serve as the U.S. ambassador to Kenya and as the CEO of Team Kenya since May of 2011," Gration said.
"However, differences with Washington regarding my leadership style and certain priorities lead me to believe that it's now time to leave."
Kenya is East Africa's largest economy and has strong ties with the United States. The two countries cooperate on military affairs and have a shared interest in containing militant threats from Somalia.
Gration spent his childhood as the son of missionary parents in Congo and Kenya, and speaks the dominant local language, Swahili. He served in the Air Force as an F-16 fighter pilot instructor, and spent two years in Kenya on assignment with the Kenya air force.
Gration was a national security adviser to Obama's first presidential campaign and served as a special assistant to the president. Before becoming ambassador to Kenya, he was Obama's special envoy to Sudan.
Gration's last day as ambassador will be July 28. It is likely the post would be filled by a charge d'affaires until a new ambassador is named after the U.S. presidential election.