By Tom Miles and Ed Cropley

GENEVA/JOHANNESBURG (Reuters) - Ethnic cleansing is taking place in some areas of South Sudan and the stage is set for a repeat of the Rwandan genocide, the head of the U.N. commission of human rights in the country said on Thursday at the end of a 10-day visit.

"There is already a steady process of ethnic cleansing under way in several areas of South Sudan using starvation, gang rape and the burning of villages; everywhere we went across this country we heard villagers saying they are ready to shed blood to get their land back," Yasmin Sooka said in a statement.

"The stage is being set for a repeat of what happened in Rwanda and the international community is under an obligation to prevent it," she said, referring to Rwanda's 1994 genocide in which 800,000 people died.

The president of South Sudan, Salva Kiir, strongly denied the U.N. allegations.

"There's no such thing in South Sudan. There's no ethnic cleansing," Kiir told Reuters in the South African city of Johannesburg. Security guards prevented further questions.

The three-person commission was set up this year and will report back to the U.N. Human Rights Council next March. Similar investigations into North Korea and Eritrea ended in calls to refer the situation to the International Criminal Court in the Hague, but neither case has reached the court.

South Sudan has spent most of its short history mired in civil war. It became independent in 2011 but rivalry between the president and his deputy erupted into war in 2013. They signed a shaky peace deal last year, but fighting and attacks on civilians continue. Much of the violence is along ethnic lines.

More than 1.1 million South Sudanese have fled the country and 1.8 million have been uprooted, most recently in the Equatoria regions, where houses are being torched and people being displaced based on ethnicity, the statement said.

The commission heard "numerous accounts of corpses being found along main roads, looming starvation and people fleeing to neighboring countries on a daily basis".

The international community needed to speed up deployment of a 4,000 strong regional protection force, ensuring its reach went beyond the capital Juba.

South Sudan also urgently needed a court to prosecute human rights abuses, the commission said.

“Large parts of the country literally have no functioning courts and even the traditional reconciliation methods are now breaking down with the result that it’s a free for all,” said commissioner Ken Scott.

Sooka described the amount of rape committed by all armed groups in the country as "mind-boggling".

“Aid workers describe gang rape as so prevalent that it’s become ‘normal’ in this warped environment but what does that say about us that we accept this and thereby condemn these women to this unspeakable fate?”

(Editing by Toby Chopra and Alison Williams)