The paper describes a novel non-contact manipulation system using an on-chip, magnetically driven micro-tool (MMT) rather than conventional biomanipulation by hand, which has a higher risk of contamination and lower success rate and repeatability. MMTs can sort particles individually, and have the unique feature that they can be installed directly in a microchannel (width = 150 μm), unlike conventional cell sorting systems. The drive unit was significantly downsized by amplifying the magnetic power using a permanent magnet. Lower power consumption could also be realized, because no energy is required to keep MMTs stationary at a particular position. Sorting was performed using real-time sensing images of microbeads, where the system successfully sorted beads of different sizes at switching speeds up to 18 Hz. The MMT developed in this study is unique with respect to its flexibility and biocompatibility; in addition, since the PDMS (Polydimethylsiloxane) microchip is disposable, it can be applied to cell sorting without any risk of contamination. Potential fields of application of this technology include cloning techniques, which require sorting of oocytes with and without nuclei.