Hamzah is also reported to be as an apologist for and friend of Abu Bakar Bashir, who is the spiritual leader for the terrorist organization Jemaah Islamiyah. While vice president, Hamzah made a public show of inviting Bashir to dinner, and visited his jihadist pesantren (religious school) in Pondok Ngruki. Hamzah denied that Bashir was connected to terrorism up until Bashir's arrest in October 2002, and was quoted as saying before Bashir's arrest "If you want to arrest Abu Bakar Bashir.. you will have to deal with me first."