This article makes a passing reference to a Soviet defector who jumped ship in 1937 in order to escape Stalin's seemingly random purges, his name was General Alexander Barmine (1899 - 1987). In his READER'S DIGEST piece from October, 1944 (the article can be read here) Barmine declared that Soviet spies were rapidly filling up positions within the U.S. Government. His more alarming proclamation was when he wrote that FDR's administration was protecting them - this implied that Red agents were already perched in the highest positions. When W.W. II ended (along with the Soviet alliance) both political parties in Washington agreed to weed out these moles - but they couldn't agree as to how deep the infiltration was. The Democrats believed that by 1953 most of the Communists had been found, the Republicans felt otherwise.
We have a few articles about the Communists who worked in government:
Read about Judith Coplon at the Department of Justice.
Read about Alfred Slack who worked at Los Alamos.
Read about Noel Field of the State Department and the OSS.
Read about Mary Jane Keeney at the United Nations.
Although no reference is made in this article concerning his espionage activity on behalf of the Soviets, the most highly placed spy within the U.S. government during the Second World War was FDR's right-hand-man, Harry Hopkins.