UN report says Aggrey Idri Ezibon and Dong Samuel Luak were likely killed by National Security Service men.
South Sudan has rejected UN allegations that its security services kidnapped two prominent government critics exiled in Kenya in 2017, flew them to Juba and days later executed the pair on a farm owned by President Salva Kiir.
A report by the UN Security Council panel of experts published late on Tuesday said multiple credible sources suggested Aggrey Idri Ezibon, a member of an opposition group, and Dong Samuel Luak, a human rights lawyer, were likely killed by National Security Service (NSS) officers on January 30, 2017.
"These people were apprehended in Nairobi, they have not been brought to us. We are not responsible for any disappearance of any South Sudanese around the world," said Michael Makuei, South Sudan's Minister of Information.
"They should first ask Kenya where these two people are and not South Sudan," he told Reuters. Idri and Dong were living in Nairobi when they disappeared in late January 2017.
Kenyan Foreign Affairs Principal Secretary Macharia Kamau declined to comment.
The UN experts said in their report the men were flown to Juba on a commercial plane chartered by South Sudan's embassy on January 27, and held in cells in the NSS headquarters, known locally as the Blue House.
Three days later, the pair was allegedly executed at an NSS training facility located on a sprawling property owned by Kiir in Luri, 20km outside Juba, on the orders of the head of the service, Akol Koor Kuc, the report said.
Their bodies have not been found.
The report concluded, based on "a number of independent reports from multiple, highly credible and well-placed sources... that it is highly probable that Aggrey Idri and Dong Samuel Luak were executed by Internal Security Bureau agents at the Luri facility".
South Sudan seceded from Sudan in 2011, but descended into a brutal civil war two years later.
Following a string of failed agreements, a peace deal was signed last September between Kiir and his former deputy turned rival Riek Machar.
The deal largely put an end to fighting and, among other things, mandates the creation of a joint war crimes court with the African Union, otherwise referred to as the hybrid court.
In a statement, Dr Machar, whose opposition group Idri worked for, renewed calls for the creation of the hybrid court, and asked for the UN to refer the alleged killing to the International Criminal Court in the Hague.
The UN panel said the National Security Service "has emerged as a significant and parallel fighting force able to operate outside the rule of law and the framework for the implementation of the peace agreement".
Rights groups say the security services have a history of detaining and torturing people, creating an atmosphere of fear and self-censorship among activists and journalists.
The government denies the accusations.
South Sudanese authorities should promptly undertake an independent and effective investigation, Amnesty International and Human Rights Watch said in a joint statement.