Optical absorption, electron spin resonance and photoluminescence spectra were used to study the defect formation in high purity fused silica induced by a focused infrared femtosecond laser with the input intensity below damage threshold. Si E centres were formed in the silica. The number of Si E centre was found increasing linearly with power density of the fs laser, deviated from the increment photo-induced free carrier density. We concluded that the colour centres were formed at the defect sites that were newly generated by radiolysis of silica tetrahedral network and displacement of oxygen between two silicon atoms. Material structure is already modified even though the irradiation fs laser power was well below the damage threshold.