The International Criminal Court said Gadhafi, his son Seif al-Islam Gadhafi and his intelligence chief Abdullah al-Sanoussi are wanted for orchestrating the killing, injuring, arrest and imprisonment of hundreds of civilians during the first 12 days of an uprising to topple Gadhafi from power, and for trying to cover up the alleged crimes.
The warrants from the court in The Hague turn the three men into internationally wanted suspects, potentially complicating efforts to mediate an end to more than four months of intense fighting in the North African nation. The warrants will be sent to Libya, where Gadhafi remained defiantly entrenched.
Presiding judge Sanji Monageng of Botswana called Gadhafi the "undisputed leader of Libya" who had "absolute, ultimate and unquestioned control" over his country's military and security forces. She said there were "reasonable grounds to believe" that Gadhafi and his son are both responsible for the murder and persecution of civilians.
Gadhafi's regime did not immediately react Monday to the announcement, but rejected the court's authority even before the decision was read, accusing the court of unfairly targeting Africans while ignoring what it called crimes committed by NATO in Afghanistan, Iraq "and in Libya now."
"The ICC has no legitimacy whatsoever ... all of its activities are directed at African leaders," government spokesman Moussa Ibrahim told reporters Sunday.
Mohammed al-Alaqi, the justice minister in the Libyan rebel administration, picked up a copy of the warrant from the court but cast doubt on rebels' willingness to turn over Gadhafi if they did arrest him. He told reporters there was nothing to prevent the rebels from putting Gadhafi and his son on trial in Libya.
"If they prosecute them in Libya it would be under the standards of this court," he said. "Let's decide later, after we arrest them, where we should prosecute them, here or there."
Al-Alaqi said he hoped the warrants would persuade Gadhafi's forces to defect.
"Maybe this decision will make the military brigades change their minds, because Gadhafi and his son have no future at all," he said.
In Brussels, NATO Secretary-General Anders Fogh Rasmussen said the court's decision highlighted the increasing isolation of the Gadhafi's regime.
"It reinforces the reason for NATO's mission, to protect the Libyan people from Gadhafi's forces," he said Monday, adding that the Libyan leader and his supporters need to realize that "time is rapidly running out for them."
NATO air forces have been conducting daily air strikes against military targets in Libya for the past 100 days - a bombing campaign that has drawn increasing international criticism.
In Tripoli, two loud explosions shook the area near Gadhafi's compound Monday, setting off a chorus of emergency sirens in the Libyan capital. Libyan officials said NATO fired two missiles targeting Gadhafi's personal bus, about 100 yards (meters) from the human shields the Libyan government keeps inside Gadhafi's Bab al-Aziziya compound.
Journalists were taken to see a heavily damaged, burnt-out bus inside the compound two hours after the strike. It didn't appear to have been struck recently, however, since it was cool to the touch. No one was reported killed in the strike, though officials said two people were slightly injured.
A coalition including France, Britain and the United States began striking Gadhafi's forces under a United Nations resolution to protect civilians on March 19. NATO assumed control of the air campaign over Libya on March 31 and is joined by a number of Arab allies.
European nations praised the warrants.
British Foreign Secretary William Hague said they "demonstrate why Gadhafi has lost all legitimacy and why he should go immediately. His forces continue to attack Libyans without mercy and this must stop."
In Paris, French President Nicolas Sarkozy said "after 41 years of dictatorship, it is perhaps time to stop, for him to leave power."
The Foreign Ministry of Italy, Libya's former colonial ruler, said the warrants confirmed that Gadhafi had "lost all legitimacy, political and moral" in both his own country and the international scene. "As such, he can have no role to play in Libya's future," it said.
Chinese Premier Wen Jiabao, however, warned that military action alone won't resolve the crisis in Libya, and said his nation backs attempts to reach a political solution in the North African nation.
"Foreign troops may be able to win war in a place, but they can hardly win peace. Hard lessons have been learned from what has happened in the Middle East and Afghanistan," Wen told reporters Monday in London.
Monageng said evidence presented by prosecutors showed that following popular uprisings in Tunisia and Egypt, Gadhafi and his inner circle plotted a "state policy ... aimed at deterring and quelling by any means - including by the use of lethal force - the demonstrations by civilians against the regime."
Hundreds of civilians were killed, injured or arrested, she said.
Prosecutors said the three suspects should be arrested quickly "to prevent them covering up ongoing crimes and committing new crimes."
"This is the only way to protect civilians in Libya," said the statement from the office of Chief Prosecutor Luis Moreno-Ocampo.
It's unclear how the warrant could restrict Gadhafi's travels within Africa, since many African states are not ICC signatories and others have declined to act on an ICC arrest warrant for another African leader, Sudanese President Omar al-Bashir. The Sudanese leader was on his way to China at Beijing's invitation when the warrant was announced for Gadhafi.
The African Union has said al-Bashir's arrest would dangerously imperil the fragile peace process in Sudan and had asked the U.N. to defer the warrant for one year. The AU's host country of Ethiopia is not an ICC member.
Gadhafi regularly attends AU summits. The AU will hold a summit later this week in Equatorial Guinea, which is also not an ICC member.
Adam Schreck in Tripoli, Libya contributed to this report