An apparatus for cleaning robotic surgical instruments includes an ultrasonic emersion tank having cleaning fluid there within and a device for providing negative pressure or suction (e.g. a pump) through a tool-end cleaning chamber. Cleaning fluid is drawn into the tool-end cleaning chamber through a plurality of intake holes in the tool-end cleaning chamber by the suction, thereby creating turbulence and flow around an end of a robotic surgical instrument that is positioned in the tool-end cleaning chamber. Cleaning of the shaft and control box of the robotic surgical instrument is performed by providing negative pressure or suction to a port on the control box of the robotic surgical instrument.
