Gemayel, a 34-year-old Christian Maronite politician, was critically wounded following an attack by gunmen in a Beirut suburb on Tuesday and died soon afterward in a nearby hospital.
"The Secretary General strongly condemns this cold-blooded murder, carried out one day after the Security Council considered the report on the establishment of the special tribunal for Lebanon," his spokesman Stephane Dujarric said in a statement.
The proposed tribunal is tasked with trying suspects in the February 2005 murder of Lebanon's former premier Rafiq Hariri. A UN probe has implicated Syrian officials in that slaying but Damascus vehemently denied any involvement.
Annan said "acts of terrorism undermine Lebanon's stability, are unacceptable and have no place in a democratic and open society."
The UN statement stressed that "the perpetrators and instigators of today's attack must be brought to justice to ensure an end to impunity" and said Annan urged all Lebanese parties "to maintain national unity at this critical moment."
The Gemayel slaying was a latest in a series of attacks on anti-Syrian Lebanese politicians over the past two years.

Copyright AFP (Agence France-Presse), 2006