Later, the UN said a news conference would be held on Monday "to mark the official launching of the intra-Sudanese Talks on Democracy and Transition".
Sudan has been shaken by pro-democracy protests and a deadly crackdown by security forces since General Abdel Fattah al-Burhan mounted the 25 October takeover that dismantled a fragile power-sharing agreement between the military and civilians.
The arrangement was agreed following the April 2019 ouster of autocratic president Omar al-Bashir after months of street protests against his iron-fisted rule.
At least 60 people have been killed in protest-related violence since the coup, according to the Central Committee of Sudan Doctors, which is part of the pro-democracy movement.
"The transition has faced major setbacks that have deeply impacted the country since the military coup," Perthes said.
"The subsequent and repeated violence against largely peaceful demonstrators has only served to deepen the mistrust among all political parties in Sudan," he added.
The UN-backed talks are aimed at "supporting Sudanese stakeholders in agreeing on a way out of the current political crisis and... a sustainable path forward towards democracy and peace," Perthes said.
The Arab League welcomed the move.
Perthes said he was "deeply concerned that the current political impasse may slide the country further into instability".
"Armed movements, political parties, civil society, women's groups and resistance committees will be invited to participate in the UN-facilitated political process," he added.
The UN Security Council is due to hold an informal session Wednesday to discuss the latest developments in Sudan.
Last week, Sudan's civilian prime minister Abdallah Hamdok resigned leaving the military in full control of the country.
Hamdok had been held under house arrest for weeks following the coup, before being reinstated in a 21 November deal after international pressure.
But the pro-democracy protest movement denounced the deal as a "betrayal", saying it provided Burhan with a cloak of legitimacy for his takeover. Announcing his resignation last Sunday, Hamdok warned Sudan was at a "dangerous crossroads threatening its very survival".