However, the evacuation exercise faced a hurdle as many Indians, who had registered with the External Affairs Ministry for leaving South Sudan, refused to return, despite an appeal by Minister Sushma Swaraj on Twitter asking them to move out. "If situation worsens, we will not be able to evacuate you," she had further tweeted.
"Operation #SankatMochan Safely out of the danger zone. The first flight makes a technical halt at Entebbe, Uganda," Minister of State for External Affairs V K Singh tweeted.
Earlier briefing reporters, MEA Spokesperson Vikas Swarup said the aim is to evacuate all the Indian nationals who have expressed their interest in leaving.
"The evacuation has been meticulously planned in coordination with the local authorities as well as the support of the Indian peace keeping contingent in UNMISS. Soon after landing, Singh met the Foreign Minister of South Sudan Deng Alor Kuol. He also met Vice President James Wani Igga."
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Both aircraft first travelled to Entebbe, Uganda for a re-fuelling halt of approximately 3 hours, Swarup said, adding from Entebbe they will depart for India, first landing in Thiruvananthapuram early tomorrow morning and thereafter coming to Delhi.
In government's assessment this was an opportune moment to arrange for the evacuation, especially since the ceasefire is holding and there is a lull in hostilities.
Singh is accompanied by Amar Sinha, secretary (economic relations) in the external affairs ministry, joint secretary Satbir Singh and director Anjani Kumar.
According to the ministry, there are around 600 Indians in South Sudan, of them 450 are in Juba and nearly 150 are outside the capital.
Later, Swaraj said that both the aircraft had taken off from Kampala and out of conflict zone.
The planes would be reaching Delhi via Thiruvanathapuram tomorrow morning, and Air India and railways would facilitate the onward journey of the evacuees.
"Both our air crafts have taken off from Kampala. We are out of the conflict zone. Both aircrafts r reaching Delhi via Thiruvananthapuram. First flight will land there around 5 am and reach New Delhi around 10 am tommw. Indian Railways and Air India will facilitate their onward journey. (sic)" she said in a series of tweets.