The report, which cited unspecified sources and could not immediately be confirmed, said the helicopter was headed toward Kazakhstan.
During the takeover, about 1,000 protesters cleared riot police from their positions outside the fence protecting the building, and about half entered through the front. Others smashed windows with stones, tossed papers and tore portraits of Akayev in half and stomped on them.
The defense minister was led out of the building by demonstrators, as other protesters threw stones at him and one kicked him. Interior Ministry troops led other officials out, and three injured people left in bandages, accompanied by a doctor.
Thick plumes of black smoke rose from the vicinity of the government headquarters, hours after some 1,000 protesters cleared riot police from their positions outside and entered the building. The source of the smoke was not clear.
Imprisoned Kyrgyz opposition leader Felix Kulov was freed on Thursday as protesters took control of key government facilities, the Interfax news agency cited opposition sources as saying.
Kulov, once a vice president under embattled Akayev, was imprisoned in 2000 under embezzlement charges that supporters said were politically motivated. His release could be a key element in unifying the Kyrgyz opposition, which until now has lacked a single clear leader.
The protests were sparked by disputed elections in February, and a second round on 13 March, which saw the opposition reduced to just a handful of seats in the 75-member parliament.
Two protesters waved a flag from a top-floor window in the building, and others looked out of other windows as cheers erupted from demonstrators. Some furniture was cast out of windows of the seven-story structure.
"I am very happy because for 15 years we've been seeing the same ugly face that has been shamelessly smiling at us. We could no longer tolerate this. We want changes," said Abdikasim Kamalov, 35, proudly holding a red Kyrgyz flag.
The storming of the compound was the culmination of the first major rally in the Kyrgyz capital since opposition supporters seized control of key cities and towns in the south to underline their demands that Akayev step down amid allegations of fraud in this year's parliamentary vote.
The rally started with about 5,000 opposition supporters moving down Bishkek's main avenue, halting in the city's main square adjacent to the white stone presidential and government headquarters. Protesters chanted "Akayev, go!"
Many of the demonstrators had come from a rally on the outskirts of Bishkek, where protesters roared and clapped when an opposition activist asserted that Akayev's foes would soon control the entire Central Asian nation.
The crowd swelled as marchers reached the government headquarters, a hulking Soviet-era building set well away from the street.
Dozens of mostly young opposition supporters soon rampaged through the government building, some smashing furniture and looting supplies and ignoring the organizers who urged them to step. Broken glass littered the floors; a drugstore in the building was ransacked.
"It's the victory of the people. But now we don't know how to stop these young guys," said Noman Akabayev, who ran unsuccessfully in the parliamentary elections.
Although the police were equipped with shields and weapons, they appeared disorganized and unwilling to take harsh action.
Many of the demonstrators wore pink or yellow headbands signifying their loyalty to the opposition — reminiscent of the orange worn by protesters who helped bring in a new, pro-Western president in Ukraine last year.
Unlike the revolutions in Ukraine, and in Georgia in 2003, the Kyrgyz uprising does not have a central figure at its head. That raises the likelihood of a jockeying for power if Akayev were to step down.
"I am concerned that for the next two months, or maybe even for a year, there will be chaos," said Iskander Sharshiyev, leader of the opposition Youth Movement of Kyrgyzstan.
Kyrgyzstan lacks the rich energy resources or pipeline routes that have made of some of its Central Asian neighbors the focus of struggles by Russia, the United States and China for regional influence. But the former Soviet republic's role as a conduit for drugs and a potential hotbed of Islamic extremism, particularly in the impoverished south, makes it volatile.
The protesters had gathered peacefully in the square outside the government building — some holding yellow Narcissus flowers to signify nonviolence — but a clash broke out when men in civilian clothes and blue armbands began throwing stones and brandishing truncheons to threaten demonstrators. Protesters retaliated by throwing stones and sticks.
The men in blue armbands — the color of the pro-government Forward, Kyrgyzstan party — chased protesters away from a platform in a central square, but demonstrators charged back and drove them away.
Two protesters were injured, one with a serious skull injury and a broken leg and another with broken ribs, said Sharshiyev.
Before the clash, Zainitdin Kurmanov, a leader of the My Country opposition party, said the demonstrators would not leave the square until Akayev resigned and called for an overhaul of the political system.
"We want to create a genuinely democratic Kyrgyzstan," he said, stressing that the protesters would not storm the government headquarters or confront police.
At the initial rally, Interior Minister Keneshbek Dushebayev addressed the crowd and urged them to obey laws. However, in a departure from his warnings the day before of a possible crackdown that could include "special means and firearms," he vowed Thursday that no force would be used against peaceful protesters.
"I promise here that force will not be used against the people," he said.
"The law is the law, and whether we like it or not we have to abide by it," said Dushebayev, to whistles and booing by protesters.