Wearing a bullet-proof vest and ringed by security, Otunbayeva encountered an angry crowd at Osh.
Al Jazeera's Clayton Swisher, who was travelling with her, said the interim leader was surrounded by a shouting mob at the end of her visit and had to be taken into a building by her bodyguards.
"The number-one complaint people had when they saw the interim president was 'What took you so long to get down here?'," he said.
Otunbayeva defended her government from criticism that it had been unable to contain the ethnic bloodshed and to cope with the escalating humanitarian crisis.
"Leave us some hope! Stop saying that we are not working," she said. "Our forces say that they are coping.
Also on Friday, Otunbayeva announced that Russia would help the country in restoring security.
"Russian troops will guard some strategic sites... to ensure security for these sites," she said.
Russia had previously refused Otunbayeva's request to dispatch military forces to help quell unrest, although the country did send humanitarian aid.
As Otunbayeva toured southern Kyrgyzstan, the UN human rights council urged the country to conduct a "full and transparent investigation" into the unrest and to hold those responsible to account.
In a unanimous resolution passed on Friday, the 47-member body also condemned "provocations and violence in Osh and Jalal-Abad".
Our correspondent said there was a heavy security presence in Osh.
"We saw security everywhere, we saw heavy road blocks. We also saw militias and individuals wearing ski masks.
"When we flow from Osh to Jalal-abad, we saw houses completely ransacked, devastated, some of them still smoldering.
"These were scenes the interim president was looking at through the window, taking all this in."
The World Health Organisation said that it was working on a worst-case estimate that the crisis in Kyrgyzstan may affect up to one million people, about a third of whom could be refugees.
Up to 100,000 people have already sought refuge in neighbouring Uzbekistan, not counting children, while about 300,000 are thought to be internally displaced, according to the United Nations.
The WHO said 700,000 more could be displaced within Kyrgyzstan but stressed that the figures were a "worst-case scenario".
Speaking to Al Jazeera from Osh, Anna Neistat, spokeswoman for the emergency unit of Human Rights Watch, confirmed reports that many ethnic Uzbek women had been raped.
"We are definitely hearing more and more horrific stories and are interviewing victims who tell us about young girls being gang-raped during the conflict and even these days."
Anna Neistat, Human Rights Watch
"I personally documented two cases of rape and received information from one of the doctors at the hospital about nine other cases," she said.
"What is most worrisome is that it continues to date.
"One of the cases I documented happened yesterday as one Uzbek woman tried to go and check on her house."
Neistat, who is in Osh to investigate allegations of human-rights abuses, said that it is hard to determine the scale of the rapes.
"We are definitely hearing more and more horrific stories and are interviewing victims who tell us about young girls being gang-raped during the conflict and even these days," she said.
Ethnic Uzbeks in Osh said that on one street alone, Kyrgyz men sexually assaulted and beat more than 10 Uzbek women and girls, including some pregnant women and children as young as 12.
Members of the Kyrgyz community have denied accusations of brutality and have accused ethnic Uzbeks of raping Kyrgyz women.
Displaced people have fled to the Uzbek border and many are now living in refugee camps in Uzbekistan.
Many are running short of water and food, crammed into clay huts and makeshift camps in the arid plains straddling the Ferghana valley.
Robert Blake, the senior US official for Central Asia, landed in the Uzbek border city of Andizhan early on Friday to meet refugees and inspect camps.
Kyrgyzstan's 5.3 million population is mainly made up of Kyrgyz (70%) ethnic Uzbeks (15%) and Russians (8%).
About 50% of the Osh region's 1.2 million inhabitants are ethnic Uzbeks.
About 40% of a population of one million in Jalal-abad region are ethnic Uzbeks.
He said an independent probe should be conducted into the violence.
"I think it's important that there be an investigation... but given the large number of ethnic Uzbek refugees here in Uzbekistan whose stories need to be heard, the Kyrgyz investigation needs to be accompanied by an investigation by an independent body," he told the news agency AFP.
Witnesses and experts say that while many Kyrgyz were killed in the unrest, most victims appear to have been ethnic Uzbeks, a community of traditional farmers and traders who speak a different Turkic language.
Ole Solvang, a Human Rights Watch researcher in Osh, said that he saw soldiers refusing to protect residents..
Solvang said Kyrgyz troops were standing about 200 metres from a neighbourhood in Osh when the looting and killings started but did not interfere.
"This is an extreme failure on the part of the government to intervene and protect these people," he said.
The riots were the worst inter-ethnic clashes to hit Kyrgyzstan since the collapse of the Soviet Union.