She said her government could not vouch for Bakiyev's security against those seeking revenge following the violence.
"To be honest we can hardly restrain those who are ready to rush there (Bakiyev's stronghold) with rifles," she said.
At least 81 people were killed when troops loyal to Bakiyev shot into crowds of opposition protesters last Wednesday during the uprising.
Bakiyev has taken refuge in the southern town of Jalalabad.
Robin Forestier-Walker, Al Jazeera's correspondent in Jalalabad, said: "I met with Bakiyev on Sunday morning. He is extremely calm and is surrounded by dozens of his supporters."
"He is calling for a UN peace-keeping force to step in and mediate between himself and Otunbayeva, and to also stop the continuing chaos that he said started after he was ousted.
"Bakiyev insists that he is still the legitimate leader of Krygyzstan."
Otunbayeva denied her team was in talks with Bakiyev and expected him to voluntarily surrender power to the interim government.
Prosecutors loyal to the new government have already opened a criminal case against two of Bakiyev's brothers and his son.
Otunbayeva said, however, that her government would not use force against Bakiyev.
"We don't support using force. The arrest warrant for his relatives and accomplices has already been issued," she said. "As for him [Bakiyev] the range of our possibilities is also becoming increasingly narrow."
On Saturday, thousands of mourners turned out in Kyrgyzstan's capital to honour those killed in Wednesday's violence.
The interim government organised funeral and memorial services on the outskirts of Bishkek, the capital, during a second day of mourning.
At Saturday's memorial services, Otunbayeva told the crowd that "those who died on April 7 are the heroes of Kyrgyzstan".
"It was our duty to establish justice. Those who are being buried here today are all our children, the children of Kyrgyzstan," she said.