Otunbayeva said that the interim government was "pretty much in control of the whole country", but warned that there could be more violence if Bakiyev stays in office.
She said she believes he is working against her from his base in the southern city of Osh.
"Bakiyev is not just sitting there and waiting," she said.
"He continues to work. Mercenaries are going through the city [Bishkek] still shooting people. They are working amongst the people, with all sorts of rumours against our interim government."
"They have enough money to work with with people against the government but we are so far controlling the situation. We must strengthen our forces day by day, and we hope to control the whole country," she said.
On Thursday, Bakiyev told Al Jazeera he would not resign. "I'm still the president," he said. "They can't do this."
But Otunbayeva announced that her interim government would run the country for six months before holding elections, and said that she was hopeful her goverment could "avoid" a wider conflict in the volatile country.
She said that life under Bakiyev had been "unbearable" and people had "zero tolerance" for detoriating conditions in the country.
Otunbayeva also confirmed that she had been in contact with Vladimir Putin, the Russian prime minister.
"I got a call yesterday from the prime minister of Russia," she said, adding that she had met with officials from the Organisation for Securty and Cooperation in Europe (OSCE) and from the US embassy in Biskek as well as officials from "other embassies".