Padayachie, aged 62, passed away in Addis Ababa, Ethiopia on Friday, where he was attending the African Peer Review Mechanism meeting of the Select Committee of Focal Points.
His body arrived in South Africa on Saturday and was handed over to his family and loved ones after it arrived in Durban from Addis Ababa.
"The body was received by the family accompanied by the Minister of Labour, Mildred Olifant, and representatives of the provincial government, representing President Jacob Zuma and Cabinet," the Presidency said.
It added that Olifant would fill the role of acting Minister of Public Service and Administration until further notice.
In honour of both Minister Padayachie and former Minister of Cooperative Governance and Traditional Affairs, Sicelo Shiceko, all national flags will from Monday fly at half-mast at all flag stations in the until the evening of burial.
Shiceka passed away at Umtata General Hospital in the Eastern Cape, on Monday, following a long illness that saw him take extended leave from his work as a minister.
Padayachie will be buried on Wednesday in Durban, KwaZulu-Natal while Shiceka will be buried on Saturday in Midrand, Gauteng.
Minister Collins Chabane, Chairperson of the Inter-Ministerial Committee on State Funerals will release further details on Padayachie, after consulting with his family.
Meanwhile, Deputy Minister of Public Service and Administration Ayanda Dlodlo has described the late Minister Roy Padayachie as a committed patriot, who "died with his boots on".
"Padayachie understood the department and was very hands on, he died without a scandal, a committed patriot and distinguished member of the African National Congress," Dlodlo said.
KwaZulu-Natal Premier Dr Zweli Mkhize described Padayachie as a leader, a community activist and struggle stalwart in a statement on Sunday.
He said community development was always on top of Padayachie's agenda.
"He was a trusted community leader who served as a crucial link between various communities and government, over the past two years. Padayachie has been working with the provincial government, together with a number of community organisations, unveiling memorial plagues across the province as part of our celebration of the arrival of Indians in the country.
"Roy served the Natal Indian Congress (NIC) with distinction, the NIC was an effective instrument that mobilised Indian workers to strike in the sugar-cane plantations, coal mines and factories.....these strikes weakened the apartheid machinery," Mkhize added.
The Premier said that the minister was determined to eradicate corruption in the civil service and he will forever be credited for his contribution towards good governance.
The Congress of South African Trade Unions in a statement said Padayachie died as he lived - working hard for his country and his continent, while on an official visit to Ethiopia.
"He devoted his life to serving his people, especially the poorest and most oppressed."
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