Otunbayeva said her temporary government was working on a new constitution to set up a parliamentary democracy in the central Asian country.
"We agreed on a parliamentary republic system and now we have a working group which is drafting a constitution," Otunbayeva said, adding that it was too early to say if she herself would run for president in elections expected in about six months.
"We didn't decide yet. I don't know so far myself," Otunbayeva said, adding that basic questions such as how the president would be elected remained to be worked out.
Otunbayeva said that Bakiyev had submitted his resignation in a hand-written letter faxed to the capital, Bishkek.
"I tender my resignation in these tragic days as I understand the full scale of my responsibility for the future of the Kyrgyz people," She read portions of the letter in a televised address to the nation.
Al Jazeera's Roza Ibragimova, reporting from Bishkek, said Otunbayeva used the address to explain why the interim government decided to let Bakiyev leave: "She said that he had become a source of instability ... and they could no longer tolerate that."
Days of turmoil
Bakiyev fled to neighbouring Kazakhstan on Thursday, ending days of turmoil.
Officials say he is in the Kazakh city of Taraz, from where he could fly on to Turkey or Latvia.
Kazakhstan, which chairs the Organisation for Security and Co-operation in Europe, confirmed Bakiyev's arrival and said it was an important step towards preventing civil war.
It said that joint efforts between themselves and Dmitry Medvedev and Barack Obama, the Russian and US presidents respectively, had allowed for the agreement for Bakiyev to leave the country.
Kazakhstan also said that the move would help to bring stability and the rule of law to Kyrgyzstan.
Since being ousted, Bakiyev had been holed up in Jalalabad where he maintains support.