U.N. leader Ban Ki-moon said the helicopter was a “clearly marked” U.N. aircraft and demanded that those responsible be brought to account.
Sudan People.s Liberation Army (SPLA) troops fired anti-aircraft guns at the Russian MI-8 believing it was a rebel helicopter carrying weapons to anti-government forces, said a South Sudan military spokesman.
The helicopter was hit while on a “reconnaissance flight” over Jonglei state in eastern South Sudan, the deputy U.N. spokesman Eduardo del Buey said in New York.
Jonglei has been stricken by ethnic strife and rebellion since South Sudan became independent in July last year with major help from the United Nations and western states. Relations have soured in recent months however.
The U.N. Mission in South Sudan (UNMISS) at first only signaled that the helicopter had crashed in the Likuangole district of Jonglei.
“Initial reports indicated the U.N. helicopter crashed and burned. The mission immediately launched a search and recovery mission. It has confirmed the death of all four crew members,” del Buey said.
“In subsequent communications between the mission and the South Sudanese armed forces, the SPLA told the mission that it had shot down the helicopter,” he added.
Ban “strongly condemns the shooting down today of a clearly marked UN helicopter by the Sudan People’s Liberation Army,” said a statement released by the U.N. in which he expressed condolences to Russia over the deaths of the crew.
“The secretary general calls on the government of South Sudan to immediately carry out an investigation and bring to account those responsible for this act,” it added.
“In light also of previous incidents, the secretary general demands that the government of South Sudan urgently puts in place reinforced measures within the SPLA to ensure that no such event may reoccur in the future.”
South Sudan military spokesman Philip Aguer said the U.N. chopper was hit by “friendly fire” and that an investigation was underway.
He said the U.N. mission had been asked whether it had an aircraft in the Likuangole region and UNMISS had replied there were none.
The spokesman alleged that the chopper was seen landing at a base belonging to rebel leader David Yau Yau.
“The plane took off while the SPLA forces were approaching the area. The SPLA artillery unit unfortunately fired on the plane,” Auer said.
“Unfortunately the plane was shot by friendly fire,” he said.
Likuangole, in the Pibor region, has been at the center of battles between rival tribes which have left thousands dead over the past year. Jonglei has also become a base for rebellion against the new government.
South Sudanese soldiers killed 14 people in the Pibor region this month in disputed circumstances.
Local officials said the victims were civilians. The army said the dead were armed followers of Yau Yau, a former theology scholar from the Murle people.
Battles between the Murle, a minority group based in Pibor, and the state's Lou Nuer majority have brought mounting strife.
Over 600 people were massacred in Pibor one year ago after an 8,000-strong mainly Lou Nuer mob went on the rampage in a district near Likuangole, according to a U.N. toll. Local officials say the figure was higher.
South Sudan’s government last month expelled a U.N. human rights investigator looking into events in Jonglei. It accused the official of producing “unjustified” and “unethical” reports.
The United Nations strongly protested to President Salva Kiir’s government over the expulsion.
Human Rights Watch and Amnesty International have condemned a string of reported abuses -- including shootings, torture and rape -- as security forces crack down on those seen to support the rebels.
Jonglei was a frontline state in four decades of near continuous civil war between South Sudan and the Khartoum government up to 2005 which left at least two million dead.
The United Nations helped organize a self-determination referendum in January 2010 and the formal split came last year. Despite substantial oil reserves, the newest state is also one of the world’s poorest.