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Francois Kanimba, a former World Bank senior economist who had been governor of the National Bank of Rwanda since 2002, was replaced by his deputy Claver Gatete.
Kagame, who has a firm grip on power in the central African country, gave no reason for the reshuffle announced late on Friday. It had been expected, however, because two ministerial posts recently became vacant.
Kagame, who has been credited with rebuilding the country since his rebel army swept to power and ended 1994 genocide, last rejigged his cabinet in December 2009.