Taylor faces a 17-count indictment by the Special Tribunal for Sierra Leone.
He is accused of arming and training rebels in exchange for so-called blood diamonds.
"Al-Qaida has been in West Africa. It continues to be in West Africa and Charles Taylor has been harbouring members of al-Qaida," David Crane, a prosecutor with the war-crimes tribunal, said on Tuesday.
Within a month of arriving in Sierra Leone in May 2002, "we ran smack dab in the middle of al-Qaida", he said.
Taylor has been harbouring al-Qaida members, including those who participated in the 1998 US embassy bombings in Tanzania and Kenya, Crane said.
"We also have activities as late as 6 April 2005," he said.
Crane specifically linked Taylor and al-Qaida to an attempt to overthrow the government of Guinea, whose president, Lansana Conte, was the victim of a 19 January assassination attempt.
Chief investigator Al White emphasised that the researchers have been "receiving credible, reliable information" on the destabilisation plans "from sources and witnesses we've been dealing with for three years in the region".
The sources report that Taylor "is actively involved in trying to destabilise the region and there will be another threat and another attempt very, very soon", White said.
"Al-Qaida has been in West Africa. It continues to be in West Africa and Charles Taylor has been harbouring members
UN war crimes prosecutor
Until Taylor is brought to justice "he will be an immediate, clear and present danger to peace and security not only in Liberia but in the entire West African region", White added.
Taylor, the former president of Liberia, is charged with war crimes and crimes against humanity by the Special Tribunal for Sierra Leone for his role in that neighbouring country's 1991-2001 civil war.
He escaped the tribunal's reach by going into exile in Nigeria in August 2003, as rebels entered the Liberian capital. He was granted asylum on condition he stay out of Liberian affairs.
The ex-Liberian president has yet to respond to the allegations.