The men, who were arrested Sunday night in a joint operation involving the CIA and Malawi's National Intelligence Bureau, were handed over to U.S. authorities Monday night, Malawi intelligence officials told The Associated Press on condition of anonymity.
The men were flown to nearby Botswana on an Air Malawi flight, the officials said. An airline official confirmed one of its planes had been chartered Monday.
Director of Public Prosecutions Fahad Assani said the men had been handed over to U.S. authorities, but said he had not been informed of their whereabouts.
Robin Diallo, spokeswoman for the U.S. Embassy in Malawi declined to comment, and U.S. Embassy officials in Botswana did not immediately return a phone call seeking comment.
Officials in Malawi said the men had been on the CIA's "watch list" since the twin 1998 bombings at the U.S. embassies in Kenya and Tanzania. U.S. authorities blame al Qaeda for the attacks.
Malawi's government has refused to discuss the allegations against the five in detail, suggesting that to do so would endanger state security.
The transfer of the men to U.S. custody came after a judge issued an injunction Monday preventing their deportation.
With no knowledge the men were already gone, the High Court ruled Tuesday that the government's attempts to deport the men without charging them violated Malawi law. He ordered prosecutors to either charge them or release them by Wednesday morning.
Prosecutors said they did not know what to charge the men with, since U.S. officials refused to share information with them. At a hearing Wednesday morning, High Court Judge Frank Kapanda ordered the men released on bail immediately.
But they were long gone.
"These people are out of reach for us. It's the Americans who know where they are," Assani told AP.
The suspects' lawyer, Shabir Latif, said the government's behavior violated the constitution.
Malawi has no extradition treaty with the United States. Authorities said the men were "prohibited immigrants" who posed a threat to national security.
While some other parts of Africa have been used as staging grounds for Osama bin Laden's terror group, Malawi had previously not been a major focus of investigations into al Qaeda.
Authorities said the men included Mahmud Sardar Issa, a Sudanese who heads a charitable organization called the Islamic Zakat Fund Trust in Blantyre. Another was identified as Fahad Ral Bahli, of Saudi Arabia, the director of the Malawi branch of Registered Trustees of the Prince Sultan Bin Abdul Aziz Special Committee on Relief.
Two of the men were from Turkey and one was an Islamic scholar from Kenya, authorities said.
Assani said that although Malawi did not have a case against the suspects, it had an obligation to help fight global terrorism.
"If the Americans have intelligence linking anyone residing in the country to terrorism, Malawi has the duty to facilitate their arrests," he said.
The poor, landlocked nation of Malawi has a 20 percent Muslim population. Africa is considered a relatively easy haven for terrorists, with its porous borders and relatively lax police presence.