Bakiyev spent about a month in a German clinic in March where he had a hip operation. His absence triggered rumors about the state of his health.
"Starting from October 20, Bakiyev will take a vacation to undergo a planned course of treatment on his legs at a clinic in Germany," the press office said.
The presidential administration did not say how long Bakiyev was expected to spend in Germany. But sources in the Central Asian state's government said the president needed more surgery followed by lengthy rehabilitation.
The impoverished ex-Soviet state, where the U.S. and Russia have air force bases, has been plagued by instability and anti-government protests since Bakiyev came to power in 2005.
Bakiyev plans to give a televised address to the nation on Friday.
