"We are launching OP #SankatMochan to evacuate Indian nationals from South Sudan. My colleague @Gen_VKSingh is leading this operation," External Affairs Minister Sushma Swaraj tweeted.
She said Singh will be accompanied by by Amar Sinha, Secretary (Economic Relations) in the External Affairs Ministry, Joint Secretary Satbir Singh and Director Anjani Kumar.
"Our Ambassador in South Sudan Srikumar Menon and his team is organising this operation on the ground," Sushma Swaraj said.
She also thanked Defence Minister Manohar Parrikar and extended her best wishes to the Indian Air Force (IAF) for providing two C-17 Globemaster heavy-life aircraft for the operation.
There are around 500 Indians in the country.
South Sudan President Salva Kiir on Monday evening ordered a ceasefire after days of heavy fighting between government troops and forces loyal to Vice President Riek Machar in Juba.
President Kiir directed all commanders to cease all hostilities, control their forces and protect civilians, Information Minister Michael Makuei said in a televised speech on the state broadcaster SSTV.
The ceasefire took effect from 6 p.m. local time on Monday any member of the Machar-led forces who surrendered must also be protected, Makuei said.
The latest bout of violence started after a localised gunfight outside Kiir's residence in Juba on July 7 when he was holding a meeting with Machar.
Earlier on Wednesday, External Affairs Ministry spokesperson Vikas Swarup tweeted that the two C-17s will take off for Juba on Thursday.
The Indian embassy in Juba said in a statement said the airccraft were expected to land at 11 a.m. local time and Indian nationals with valid travel documents will be allowed to board.
The return flights will be only up to New Delhi, the statement said.
The UN has said 36,000 South Sudanese civilians have fled their homes due to the fighting.
Embassies and aid organisations in South Sudan are moving to evacuate staff from Juba amid the tenuous ceasefire.
The US military in Africa said it has sent 40 additional soldiers to Juba to help secure American personnel and facilities in the war-torn city, Fox News reported.
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