The whereabouts of President Askar Akaev remain unknown -- but unconfirmed reports said he has left the capital and may be heading out of the country.
Prominent opposition figure Feliks Kulov has promised security for Akaev and his family.
"I hope that people close to [Akaev] will find him. And I assure you that he will have our protection and we guarantee safety for him and his family," Kulov said.
Demonstrators today succeeded in freeing Kulov -- a former interior minister and one-time mayor of Bishkek -- from prison, where he was serving a controversial seven-year term for embezzlement.
Speaking on national television after his release, Kulov called on the opposition to pursue legal means in seeking power.
"This problem should be resolved by constitutional means so nobody can reproach us that the people who have gathered here cannot solve their problems in a civilized way," Kulov said.
Another leading opposition figure, Topchubek Turgunaliev of the People's Movement of Kyrgyzstan, said the transitional government would be formed quickly and represent many interests.
"This will be a transitional government, or a government of national salvation, or a coalition government which will include many political parties, mainly those from [the opposition coalition]," Turgunaliev said.
The protesters stormed the presidential compound after a rally earlier in the day turned violent. The police initially tried to resist the protesters' advance and then fled.
RFE/RL correspondent Jean-Christophe Peuch was on the scene. He said protesters initially started ransacking the compound.
Later he toured the building and said the damage was extensive:
"Inside the White House, it is a very sad picture because the entire place has been ransacked and despite the heavy guards that have been posted everywhere [by the opposition], at every floor, we could see people stealing computers, printers, and all the cabinets are empty, basically," Peuch said.
The demonstrators also occupied the main Kyrgyz state radio and television building and immediately began broadcasting scenes from the protest. State radio halted its official programming and began broadcasting programs of the Kyrgyz Service of RFE/RL.
The Bishkek protests followed large demonstrations in other major cities, such Jalal-Abad, Osh, and Batken.
The protests were aimed at forcing Akaev out of office and re-running parliamentary elections that were widely viewed as fraudulent. The elections -- in February and March -- left the opposition almost powerless.
Russia's government meanwhile has urged Kyrgyzstan to return to a "lawful" path. The Foreign Ministry said that Thursday's events had been a cause for serious concern.
Russia had closely watched events in the former Soviet republic -- especially following recent "people power" revolutions in Ukraine and Georgia.
Russia had initially opposed both of those revolutions -- and had appeared to give tentative backing to Akaev in the run-up to parliamentary elections.
(with agency reports)
Will Opposition Leader Bakiev Be Kyrgyzstan's Next President?
Neighboring Opposition Movements Keep Close Eye On Kyrgyz Events
Photo Gallery: How The Protests Unfolded In The South
For more on the Kyrgyz elections, see RFE/RL's dedicated website Kyrgyzstan Votes 2005