The IED, planted on a road between Khordak and Arong Khong, was exploded through remote controlled device while the personnel of 33rd Assam Rifles battalion were patrolling the area at about 1.35 pm.
A Junior Commissioned Officer (JCO) and a naik subedar were seriously injured and admitted to Leimakhong Army Hospital.
Additional forces were sent to the area and all exit points sealed, the sources said.
No individual or group has claimed responsibility for the explosion which occured in the midway of the general strike called by seven insurgent organisations protesting against Manipur's merger with the union of India on October 15, 1949.
Markets, shops, banks, schools, colleges and entertainment houses remained closed while transport services between Manipur and neighbouring states and within the state were cancelled in view of the strike.
Attendance in government offices was almost nil, the sources said.