From 1995–1996, he was head of Training Division of the Israel Security Agency (ISA) also known as Shin Bet. From 1996 to 2000, Dekel was an ISA division head for planning and commanding special operations in counter terrorism and counter espionage. From 2003–2005, he was the Deputy Director of ISA, commanding and managing counter terrorism operations. From 2000-2003, he was the head of the West-bank Division, known as Central Command. This included counter terrorism activity in Jerusalem, Judea, and Samaria from the beginning of the Second Intifada.