Several international media reports had spoken of Malta as a possible destination for Gaddafi, whose whereabouts on Monday morning were unknown. Rebel fighters were in control of most of the Libyan capital Tripoli after a rapid advance on Sunday.
"Should Colonel Gaddafi or any wanted Libyan government officials come to Malta, they will be arrested and transferred immediately to The Hague", a Foreign Ministry spokesman told Reuters.
The government also said Prime Minister Lawrence Gonzi had congratulated the Libyan people on its march "towards freedom and respect for human rights" in a phone call to Mahmoud Jibril, chairman of the Libyan National Transitional Council.
Gonzi reiterated Malta's support for the rebuilding of Libya as a modern, democratic country based on freedom, justice and human rights.