Certain aspects relate to systems and techniques for driving axial motion of a shaft of a medical instrument using a drive device. Axial motion can include insertion and/or retraction of the instrument. For example, a robotic medical system can include a medical instrument comprising an instrument base and a flexible shaft configured for insertion into a patient, and a first robotic arm attachable to the instrument base of the medical instrument. The system also includes a drive device configured to engage the flexible shaft, and a second robotic arm attachable to the drive device. The second robotic arm is configured to operate the drive device to drive axial motion of the flexible shaft, and the first robotic arm is configured to move in coordination with operation of the drive device.