"The existence and activities of Lebanese and non-Lebanese militias ... continue to pose a threat to the stability of the country," Ban said.
"The presence of weapons in the country outside government control and the continued existence of militias contribute to tensions and insecurity in Lebanon and beyond, and could eventually lead to the resumption of hostilities unless immediately addressed," he warned.
The secretary-general said he took seriously recent reports "of a proliferation of extremist groups activities and of arms in Lebanon," but said the UN does not have the means to independently verify them.
He said Hizbullah's independent paramilitary force "poses first and foremost a key challenge to the safety of Lebanese civilians, and to the government's monopoly on the legitimate use of force.
"I call on the leaders of Hizbullah to complete the transformation of the group into a solely Lebanese political party," Ban said.
"Regional parties that maintain close ties with Hizbullah must encourage it in the same direction," he added.
Ban also expressed great concern at the continued presence of Palestinian paramilitary groups - the Popular Front for the Liberation of Palestine-General Command and Fatah al-Intifadah - outside refugee camps near Lebanon's border with Syria.
He said he has called on the government to dismantle four Palestinian military bases along the Lebanese-Syrian border and a fifth base south of Beirut.
Ban said the disarming and disbanding of all militias should "take place through an inclusive political dialogue that addresses the political interests of all Lebanese, and ultimately confirms the sole political and military authority of the government of Lebanon."
The secretary-general urged all countries to abide by the UN arms embargo against militias, saying "this is a key factor for stability in Lebanon and the region."
Ban called the June 2009 parliamentary elections "another milestone" in Lebanon's commitment to democracy and urged the country's leaders - who have not been able to form a government - to "transcend sectarian and individual interests and promote the future and the interests of the nation."
He also praised the establishment of diplomatic relations between Lebanon and Syria and urged both countries to mark their border.