Her comments on Friday came as funerals were being held throughout Bishkek on the first of two days of mourning for the more than 75 people killed in Wednesday's violent demonstrations.
Al Jazeera's Robin Forestier-Walker, reporting from Bishkek, said the capital was "calm".
"The interior ministry is now under control of the so-called interim government; they are co-operating; they say the situation is stable".
Otunbayeva told Al Jazeera 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 believed he is working against her from a base in Osh.
"Bakiyev is not just sitting there and waiting," Otunbayeva 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 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.
Vigilante groups, hastily organised by the interim government, spent Thursday night fighting looters in a bid to restore stability.
Sporadic gunfire was heard throughout the night but a government spokesman said nobody was killed.
"It is quiet again in the capital. No one died overnight," Abdykalyk Ismailov, the interior ministry spokesman, said. "There are still some groups of looters but the city is largely under control."
Bruce Pannier, a journalist and expert on Kyrgyzstan, told Al Jazeera that the interim government was enjoying support in areas that had traditionally supported Bakiyev.
"They seem to have support around the country. Certainly Bishkek has settled down and reports coming out of the south indicate that by and large, everyone is behind the new government that has been established here," he 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 said that her interim government would now run the country for six months before holding elections.
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 Security and Co-operation in Europe (OSCE) and from the US embassy in Bishkek as well as officials from "other embassies".
Meanwhile, the US air base in the country had resumed normal operations after flights were cut back due to the violent protests in the capital.
In the interview with Al Jazeera, Otunbayeva dismissed rumours that she was planning to close the Manas base, which supplies military operations in Afghanistan, as "speculation"
"We will keep our commitments to those agreements that were signed earlier," she said, adding that her government's priority was to provide security and "return life to normalcy" for people of the country.
Omurbek Tekebayev, a former Kyrgyz opposition leader in the provisional government, had said on Thursday that the duration of the US air base's lease could be shortened.