In 1999 Eizenkot was selected to be the Military Secretary for the Prime Minister and the Minister of Defense under then Prime Minister Ehud Barak. Since then he has commanded the 366th Division and the Judea and Samaria Division, where he led the Campaign against Palestinian political violence. He was promoted to head of Israeli Operations Directorate in June 2005. After the conclusions exercise "joining of forces" Eizenkot led the formulation of the concept on which the IDF must severely damage the center of gravity of Hezbollah, the Dahiya neighborhood, as a key component for creating deterrence against Hezbollah. During the Second Lebanon War he was one of the few generals of the General Staff who dared to disagree with the Chief of Staff, Dan Halutz, and the measures proposed. Among other things he argued, at the beginning of the war, that the IDF must raise the reserve forces to improve preparedness for a large-scale ground offensive, and stressed that Israel must strive for a quick end of the war.