An investigation is underway to ascertain whether the incident was a case of mistaken identity.
Speaking to Manorama News, Lt Colonel Nair said the insurgents have the backing of China.
Myanmar's junta said on Friday they would hold elections within two years, the first timeframe it has given for a return to democracy since its February 1 coup.
India shares a 1,600 km land border with Myanmar, where more than 50 people have been killed during protests against the coup.
Protests that swept the country on Sunday were the biggest since a 2007 Saffron Revolution led by Buddhist monks that helped prompt democratic reforms that were upended by the February 1 coup.
The two sides might launch the third phase of the operation, depending on intelligence inputs and the ground situation.