The Manhattan Project was created in 1939 prior to the United States entering the war. It continued on until even after the bombs were dropped on Japan and the war ending. However, it may seem unusual that the American government would continue to have this group around, but they did. The Manhattan Project disbanded in 1947 a couple of years after the end of World War II. Besides the war being over and this military group being behind the bombing, there may have been no need to keep this expensive group around.
Also, many people were upset with the bombing on Japan because it killed many innocent adults and children in horrific deaths. Therefore, the government may have believed it would be best to disband it.