The IAF said that Gen Rawat, his wife and 11 other persons died in accident.
Prime Minister Modi, Defence Minister Rajnath Singh, Home Minister Amit Shah, Finance Minister Nirmala Sitharaman and External Affairs Minister Dr Subrahmanyam Jaishankar attended CCS meeting.
The chopper took off at 11.48 am from the Sulur Air Base and was reported to be missing at around 12.22 pm, sources informed.
India recognised acts of gallantry by armed forces personnel and senior military officers involved in Operation Sindoor, along with other distinguished service awards, on the eve of the 79th Independence Day.
Out of the 13 people killed in the IAF helicopter crash near Coonoor on Wednesday, the mortal remains of only Chief of Defence Staff Gen Bipin Rawat, his wife Madhulika Rawat and Brig LS Lidder could be identified, officials said on Thursday.
The armed forces personnel whose bodies were identified in the last few hours are Junior Warrant Officer (JWO) Pradeep, Wing Commander P S Chauhan, JWO Rana Pratap Das, Lance Naik B Sai Teja and Lance Naik Vivek Kumar.
Prime Minister Narendra Modi on Thursday visited the Palam airbase in New Delhi and paid his last respects to Chief of Defence Staff General Bipin Rawat, his wife Madhulika Rawat and other 11 armed force personnel who lost their lives in a chopper crash in Tamil Nadu on Wednesday.
Chief of Defence Staff Gen Bipin Rawat, his wife Madhulika Rawat and 11 others were killed when an Indian Air Force helicopter carrying them crashed on Wednesday near Coonoor in Tamil Nadu in apparently foggy conditions, killing 13 people on board, the IAF and other officials said.
To ensure the morale of the pilots does not suffer, flying activity continues without a pause. Pilots take to the sky like they would on any other day.
Singh said in a statement in the Lok Sabha that all efforts were being made to save IAF Group Captain Varun Singh, the lone survivor of the crash near Coonoor in Tamil Nadu on Wednesday, who was on life support at the military hospital in Wellington.
The mortal remains of six soldiers martyred in Manipur last week belonging to Jammu region of the state were cremated with full military and state honours on Sunday.
The plaintive strains of bugles sounding the last post broke through the hush, men in uniform clicked their heels and a 17-gun salute rang out as Gen Bipin Rawat and his wife were cremated on Friday evening -- the sun setting on a day written into India's military history and on the life of its most senior military officer.