Otunbaeva, speaking at a media conference in Bishkek, said the explosion shows that democracy is in danger in Kyrgyzstan.
"I think this has the handwriting, the attitude, of the government toward the opposition," Otunbaeva said. "Not only the [independent] press, but [the whole of] democracy is in danger in this country. But we will not give them any chance [to ruin democracy]."
Presidential press secretary Abdil Segizbaev denied any government role and said an investigation has been launched. He told RFE/RL's Kyrgyz Service that he believes Otunbaeva is using the incident as a provocation.
"Ms. Otunbaeva made her statement [at the Bishkek forum devoted to protection of independent mass media]," Segizbaev said. "She talked about the bomb, grenade, etc. But this is worth nothing. This is [just] a provocation. She wants to make her name known, she wants to incite people. Her statement was made in such a mood."
Otunbaeva said the apartment was damaged but no one was injured.
"Today at five in the morning, a grenade was detonated at my flat in a house," Otunbaeva said. "There was damage to the flat as well as to [the other flats in the building]. Windows were broken in this old house where I live."
The incident came in the wake of the country's 27 February election, in which government-backed candidates generally fared well, but which outside observers have criticized. The Organization for Security and Cooperation for Europe, which monitored the vote, said it fell short of democratic standards.
Kyrgyz authorities prevented Otunbaeva -- an outspoken critic of President Askar Akaev -- and other prominent opposition members from running in the election. The authorities claimed she was ineligible since she had not resided continuously in the country over the last five years.
Prior to the election, Otunbaeva -- inspired by Ukraine's Orange Revolution -- had urged her supporters to wear yellow. This angered many in the government who saw it as a call to revolution.
Otunbaeva's nephew, Ulanbek, said before the explosion that a dollar sign was painted on the wall outside Otunbaeva's apartment. This may have been an attempt to discredit her by implying that her party is financed by the West.
"What I know is that in the this same night before the explosions, a sign appeared on the facade [of the building] -- the dollar sign," Ulanbek said. "This has already happened in our city couple of times and is publicly known that this kind of sign is put on opposition members' homes by provocateurs."
It's not known when the results of the investigation will be made public.
(RFE/RL's Kyrgyz Service contributed to this report)