The death of senior Ugandan rebel Vincent Otti could hamper peace talks aimed at ending the 20-year conflict, government minister Okello Oryem says.
There has been speculation over Mr Otti's fate since November 2007
Otti, second in command of the Lord's Resistance Army rebels, was reportedly killed by LRA commanders last year.
But his death was only officially confirmed by the LRA earlier this week.
"Now that he is dead it leaves a huge gap on the LRA's side," the minister for international affairs said ahead of the talks that are to resume on Monday.
The conflict has killed tens of thousands of people and uprooted some 2m people.
South Sudan's deputy President Riak Machar, who is mediating the peace talks, confirmed Otti's death on Tuesday after meeting an envoy from LRA leader Joseph Kony.
Until then, the LRA had insisted Otti was alive and under house arrest - accused of being a government spy.
But a diplomatic briefing in December, based on witness testimony, alleged Otti was executed by fellow officers on Mr Kony's orders.
"[The killing] erodes trust in Kony and will definitely choke the talks when we resume next week," Reuters news agency quotes Mr Oryem as saying.
Commentators say Otti played a key role in initiating the talks which began in July 2006.
Otti was one of four other LRA commanders wanted by the International Criminal Court (ICC) for war crimes committed during their insurgency.
Mr Kony, who has also been indicted, is in hiding in the remote north-east of the Democratic Republic of Congo.
The LRA were notorious for mutilating victims and kidnapping children to be fighters, porters and sex slaves.