Security officials said that on Friday two armoured vehicles from the UN Interim Force in Lebanon, a 2,000-member peacekeeping force deployed in southern Lebanon, headed to Marjayoun, which Israeli forces occupied on Thursday.
They will escort the Lebanese soldiers out of their barracks in a convoy that will take them into government-controlled territory further north, the Lebanese security officials said.
On Thursday, Ahmed Fatfat, the interior minister, said Israeli soldiers entered the garrison in the afternoon "and asked to share it with Lebanese troops there".
He said the soldiers refused and wanted to leave, but the Israelis stopped them.
"They [Israelis] say they are searching for heavy weapons that might endanger them or that there are resistance fighters in the barracks. But our impression is that they might have wanted to use the Marjayoun barracks as a kind of human shield," he said.
"We consider them captives," Fatfat said, adding that the government was trying to win their release.
Israel said the soldiers had been prevented from leaving for their own safety.
Lebanese and Arab media reports said that France and the US intervened to arrange for the evacuation of the Lebanese soldiers.
There are more than 1,000 Lebanese soldiers in southern Lebanon conducting security duties. But Hezbollah fighters actually control the south.
The government has pledged to send 15,000 soldiers to the border with Israel as part of a peace package to end one month of fighting and bombardment by Israel.
Israel has insisted on staying in southern Lebanon until an international force is deployed, which could take weeks or months.