Hamzah served as Minister for Investment under President B. J. Habibie, who replaced Suharto, then resigned that post to lead the PPP in the 1999 elections, at which he was again reelected.

In 2002, Bill Guerin, in an opinion piece in the Asia Times wrote, "Hamzah ... is widely seen as blatantly vying for support from among Indonesian Muslims, including the militant groups, to strengthen his run for the presidency in the country's next general elections in 2004.

[citation needed] While vice president, Hamzah made a public show of inviting Ba'asyir to dinner, and visited his jihadist pesantren (religious school) in Pondok Ngruki.

"[6] In October 2002, an article in Time stated "That clerics like Abu Nakar [Ba'asyir] have powerful military and political allies is no secret: the nation's vice president Hamzah Haz is one of them."

Hamzah, although he "has a reputation as a wily politician" nevertheless "will be remembered for a particularly ill-judged speech before Muslim clerics at Abu Bakar's Solo boarding school in May [2002]", the newsmagazine reported.

[7] In 2002, an Australian academic cited Hamzah as the "best example" of Islamic politicians in Indonesia "prepared to play the extremist card to attract extra votes".

Hamzah "has supported Jemaah Islamiyah and has even been instrumental in having its members released from detention in the past", according to Tim Lindsey, director of the Asian Law Centre at the University of Melbourne.

In a voice-over played during the television interview, an ABC journalist said, "Before the Bali bombing, Vice President Hamzah Haz insisted there were no terrorists in Indonesia.

After the bombing, he gave this extraordinary justification for that position:"[9] The ABC interviewer then told Hamzah: "In light of Bali, that would seem a reprehensible comment, if you knew that people were here."

[19] He was disciple of Idham Chalid, a charismatic South Kalimantan Ulama and politician, and received political, religious, and spiritual training and guidance from him.

[19] Sometimes known as Dr. Hamzah, he was reported to have obtained a PhD from American World University, an internet diploma mill (institution which improperly sells academic degrees), for US$1,200.