The incident took place in the 10 Sikh Light Infantry regiment during an inter-company boxing match there, sources said in New Delhi.
The Army Headquarters said a Brigadier-level officer has been tasked to conduct a Court of Inquiry into the clash.
The Lt Col, who is the second-in-command of the unit, has been hospitalised in the local military health facility after he was beaten up by the jawans after they felt they were being discriminated against, the sources said.
Army Chief Gen Bikram Singh also belongs to the Sikh LI regiment. The 10 Sikh LI is based in Delhi and is in Meerut for practice, Army officials said.
The Army tried to downplay the incident, saying in contact sports such as boxing, emotions and passions run high and sometimes result in such clashes and officers and men have not been separated.
In the last couple of years, the number of clashes between officers and jawans has gone up considerably.
On August 8, 2012, jawans agitated against the commanding officer and certain functionaries of the 16 cavalry unit in Samba, while on May 10-11, 2012, a case of manhandling involving officers and other ranks of the 226 artillery unit took place at the Mahe field firing range in Leh, he said.
On April 29, 2010, an altercation had taken place between an officer and a jawan of the 45 cavalry unit in Gurdaspur.
The army has already taken steps against its personnel in these cases and more than 200 officers and jawans have faced disciplinary or administrative action last year.
After incidents of clashes between officers and jawans, Army commanders have been told to exercise zero tolerance in such cases and exemplary punishment is promulgated to give "necessary preventive lessons" to the personnel.
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