"Negotiation started," the ministry said in a statement, adding that the regional East African bloc IGAD "was committed to support in any way possible".
The two sides are meeting with special envoys from regional nations, with sources suggesting the rivals may not meet directly until at least tomorrow.
Government and rebel negotiating teams had begun arriving on Wednesday at a luxury hotel in Ethiopia's capital Addis Ababa, but the start of talks had been delayed until the full teams arrived.
Thousands of people are feared to have been killed in the fighting, pitting army units loyal to President Salva Kiir against a loose alliance of ethnic militia forces and mutinous army commanders nominally headed by ex-vice president Riek Machar.
Aid workers have increased warnings of a worsening crisis for civilians affected by the conflict, which some observers have warned risks deteriorating into full-blown civil war.
Fighting erupted on December 15 when Kiir accused Machar of attempting a coup in the world's newest nation.