MPs voted 232-179 for an inquiry into alleged links between Mrs Ciller and contract irregularities at the state-run electricity distribution company, TEDAS. Approval of the motion in a secret ballot suggested that deputies from Mrs Ciller's new coalition partner, Motherland Party (ANAP), had abandoned her.
She has warned that the conservative coalition government could collapse if ANAP joined the opposition ranks against her.
"The commission will work for two months,"deputy speaker Kamer Genc told the 550-member assembly.
Mrs Ciller, who became Turkey's first-ever woman prime minister in 1993, stands accused of enriching herself, her husband and their associates through manipulation of contracts and privatisation.
"Mrs Ciller's biggest mistake was not preventing her husband from interfering with state contracts and appointments," Islamist MP Sevket Kazan, the architect of the corruption motion, told the parliament.
The commission could recommend taking Mrs Ciller to the Supreme Court, which would effectively ruin her chances of becoming premier again under a power-sharing deal with the Prime Minister, Mesut Yilmaz.
Mrs Ciller stepped down in March after inconclusive general elections late last year in which the Islam-based Welfare Party won by a the narrowest of margins. She was not in parliament for the vote.
The refusal of Mr Yilmaz, leader of ANAP, to rally to Mrs Ciller's defence has renewed doubts about the minority coalition's longevity.
Mr Yilmaz, a political soulmate of Ciller but a bitter personal rival, told his deputies to vote with their consciences.
Mrs Ciller called the vote "a political manoeuvre", but refused to comment on whether her coalition was in danger of crumbling, given the support by some of its members for the investigation.
"There's anger in my party. I will try to calm my friends down," said Mrs Ciller
In a separate vote, parliament decided also to investigate former energy minister Sinasi Altiner for the same charges.