Khandu, accompanied by the sister of Tawang MLA, security officer, had taken off from Tawang at 9:56 am and was to land at Itanagar at 11:30 am by a Pawan Hans helicopter Eurocopter B3 craft. Tawang is about 200 kms from Itanagar.
The chopper was last in communication with the base when it was overflying Sela Pass, 20 minutes after taking off from Tawang, and all communications were lost after that.
There was confusion in the afternoon with claims made by Governor Gen (retd) J J Singh first and then by the Chief Minister's Office and defence spokesperson that the Chief Minister chopper had landed safely in a place called Daporijo in Upper Subansiri district.
The Arunachal Pradesh government has formed a crisis management team to monitor the situation. After the incident, a high level emergency meeting was held at CM's office which was attended by ministers, MP Takam Sanjay and senior officers, including Chief Secretary Tabam Bam and IGP SBK Singh.
The meeting set up a crisis management cell with principal secretary to CM Yeshi Tsering, civil aviation commissioner Hage Khoda, home secretary A K Srivastav, IGP SBK Singh, DIGP (West) Robin Hibu, DIG(Intelligence) Anil Shukla, City DC Pawan Kumar Sain and SP Apang Tamut. The committee will be monitoring the situation under the overall guidance and supervision of Chief Secretary Tabam Bam.
The CM's office said the helicopter had landed in a place in Bhutan. However, later in the evening there were denials from all concerned saying helicopter has not been located and search operation was still on.
"The helicopter is missing and the search operation is still on," Union Home Secretary Gopal K Pillai said in New Delhi in the evening.
The Arunachal Pradesh government said that it is yet to ascertain the whereabouts of the Pawan Hans chopper which went missing since morning with the Chief Minister and four others on board.
Arunachal Pradesh Deputy Inspector General of Police Robin Hibu said joint search operation for the missing copter will be conducted by army, air force and state police from Sunday morning by air and through ground.
The five on board included crew members Captain J S Babbar and Captain K S Malick, Khandu's security officer Yeshi Choddak and Yeshi Lamu, sister of Tawang MLA Tsewang Dhondup.
Defence spokesman Wing Commander Ranjeev Sahoo said in Shillong that two IAF Cheetah helicopters were sent for the rescue and search operations.
"They have flown from Tezpur and searched the route from Tawang to Itanagar. Because of inclement weather they had to come back after two hours of search. But they could not locate the missing chopper. If needed they would be sent again tomorrow," Sahoo told PTI.
Pawan Hans officials said in Guwahati, "We have not been able to contact our pilots and unless we receive information from them, we cannot confirm any report".
56-year-old Khandu, who had served in the intelligence wing of the Indian army, was sworn on April 9, 2007 as the fifth chief minister of the state, replacing Gegong Apang.
Earlier Pillai had said that search parties left from Itanagar by road to the probable site near Sela Pass. The defence ministry, army and the air force have all been alerted.
"Unfortunately because of very bad weather the flights have not been able to take off for the search in Tawang area. But as soon as weather clears, the helicopters will take off", Pillai said.
Defence ministry spokesman in Kolkata, Wing Commander Mahesh Upasani said despite inclement weather, two Cheetah helicopters have been pressed into service from Tezpur in Assam for search and rescue operations.
The request for help reached the air force at 1230 hours and the two helicopters took off within 40 minutes. The air force has pressed into service two helicopters in search operations to locate the missing chopper.
The Pawan Hans chopper was a Eurocopter B-3 and was just 4-5 months old. It was based in Itanagar.
This is the third helicopter to get into trouble in the Northeast in the last fortnight. In the April 19 incident, a Pawan Hans helicopter crashed in the mountains of Tawang, bordering Tibet, killing all 17 people on board.
The helicopter crashed not far away from the helipad and the DGCA had found that proper fire-fighting facilities could have saved lives.
In the other incident, an army helicopter crashed near Gangtok killing four occupants on board.
The chief of Bhutan Police in a statement to television channels denied any landing of chopper within the country's territory.
India's Ambassador to Bhutan Pavan Verma said Bhutan has not reported any landing of an Indian helicopter in its territory.
"There is no confirmation of a landing of Indian chopper in Bhutanese territory," he said. Bhutanese personnel are carrying out a recce on the ground and the government has alerted local authorities in seven districts in the hilly country sharing the border with Arunachal Pradesh.
With inputs from K Anurag in Guwahati