Among those rescued from the conflict zone were two Nepalese, seven women and three children.
The evacuated Indians came in an Indian Air Force (IAF) C-17 Globemaster heavy-lift aircraft that first landed at Thiruvananthapuram airport around 5 a.m. and then in Delhi at 10.45 a.m.
Of the 156, 85 deplaned at Thiruvananthapuram and 71 landed at Delhi.
Prime Minister Narendra Modi welcomed the evacuated Indians and congratulated Defence Minister Manohar Parrikar, the IAF, and the Railway Ministry for their effort. He also congratulated External Affairs Minister Sushma Swaraj and Minister of State for External Affairs V.K. Singh, who led the operation.
"PM congratulated RM @manoharparrikar, IAF, the Railways, @airindiain for their role in Operation #SankatMochan," PMO India tweeted.
Indian Railway Catering and Tourism Corporation (IRCTC) made special arrangement for the onward journey of the persons belonging to Maharashtra, Uttar Pradesh, Kerala, Delhi, Chandigarh, Odisha, Tamil Nadu, Telangana, West Bengal, Rajasthan and Andhra Pradesh.
"We have been providing free AC third class tickets to the Indians evacuated from South Sudan to sent them their native states," Deputy General Manager (IRCTC) Achyut Singh told IANS.
Naveen, 34, one of those who returned here, told IANS that he could not come out of his home in Thongpiny area in Juba, the capital of South Sudan, since Friday when he heard gunfire outside.
"My neighbours residing there also faced the same situation and they are still stuck inside their homes. I heard news that the Indian government wanted to evacuate Indians from Juba. I approached the Indian embassy and have come back."
Another Indian, Anil Kumar told reporters that firing had intensified in South Sudan early this week.
"For almost five days there was heavy firing and it was then that we decided to return. Yesterday it was a quiet day, that made our movement to the airport easy," said Anil Kumar.
On arrival at Delhi, Singh said: "We've brought back 156 Indian nationals, of whom 85 deplaned at Thiruvananthapuram airport. I met Foreign Minister (Barnaba Marial Benjamin) and Vice President (Riek Machar) of South Sudan and they assured me of all possible help," Singh told reporters after landing in the capital.
"Over 300 Indians will continue to stay in South Sudan for their business interests. About 150 Indians work in the oil wells, and for them it's easier to go towards Sudan where there are not much issues," Singh said.
"While I was there, I spoke to the Vice President of South Sudan and he told me what they are doing with regard to the safety of the people there," added Singh.
In Thiruvananthapuram, Minister for Electricity Kadakampally Surendran and district officials received the evacuated Indians at the airport on behalf of the Kerala government.
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