The departure came only two days after Bakiyev arrived in Kazakhstan under the mediation of Russia, Kazakhstan and the United States.
Bakiyev confirmed in a televised address on Friday that he was in Kazakhstan.
"I would like to express my sincere gratitude to you for your help and care about me," Bakiyev said to Kazakh President Nursultan Nazarbayev in the address.
Bakiyev fled to southern Kyrgyzstan last week after thousands of protesters supportive of the opposition clashed with security forces throughout the country, driving out local governments and seizing government headquarters in Bishkek.
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