Michalis Sarris will be replaced by Labour Minister Haris Georgiades, reports in the local media suggest.
The 10 billion-euro ($13 billion) deal – agreed by the EU and IMF – originally envisaged a levy on all Cypriot bank depositors, triggering public anger.
Under the revised deal, Bank of Cyprus depositors with more than 100,000 euros could now lose up to 60% of their savings.
On Tuesday, Cyprus’ government said that President Nicos Anastasiades had accepted the resignation of Michalis Sarris, who had been under fire for his handling of the bailout deal.
Nicos Anastasiades earlier ordered an investigation into what led Cyprus to the brink of bankruptcy before it was forced to accept tough bailout conditions.
The inquiry will be carried out by a three-judge panel.
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