Irina Kamarda said that none of those being tried in absentia -- including the former president and several others -- has ever been questioned and no personal statements regarding the charges against them have been recorded to be considered by a court.
She said that therefore "the trial cannot be considered legal" and judge Damir Onolbekov should be replaced.
After Kamarda's statement, the trial was adjourned until an unspecified date.
The trial of Bakiev and 27 other former top Kyrgyz officials had resumed on March 18 after a four-month break.
Bakiev and his former associates are accused of having fired upon, or given the command to open fire on, unarmed protesters in Bishkek during the protests.
Many of the defendants are jailed or under house arrest, while Bakiev and several other defendants are being tried in absentia. Bakiev lives in Belarus at the invitation of President Alyaksandr Lukashenka.
The trial is being conducted by the Bishkek garrison's military court at the Department for Penitentiary System Control. Hundreds of police are present at the trial to prevent disturbances.
Read more in Kyrgyz here