Dingko Singh was arrested by Imphal Police last evening for hitting a female athlete at the Khuman Lampak sports complex in Imphal on Monday.
The boxer was posted as a SAI coach at its Imphal centre since December last year.
"SAI has placed him under suspension with immediate effect pending inquiry. It's a serious matter," Thomson told PTI.
Dingko surrendered to police yesterday after the family members of the female athlete registered a case against the boxer for hitting her with a stick.
Dingko won the gold medal at the 13th Asian Games held in Bangkok in 1998 for which he received the prestigious Arjuna Award and was conferred the Padma Shri last year.