The announcement came hours after the army declared a pause in its nine-day assault on IS in exchange for information on the missing soldiers.
Head of the General Security agency Major General Abbas Ibrahim said IS fighters who had surrendered led his agency and the Lebanese army to the remains.
"We have removed the remains of six bodies. We are expecting the number to go up to eight," he told reporters gathered in downtown Beirut.
The army later released a statement saying the remains of eight bodies had been retrieved from the Jurud Arsal mountainous border area with Syria and taken to a military hospital for DNA testing.
The troops were among 30 soldiers and police kidnapped by IS and Al-Qaeda's former Syrian affiliate when they overran the Lebanese border town of Arsal in August 2014.
Four were killed by their captors and a fifth died of his wounds while 16 were released in a prisoner swap in December 2015 that was also overseen by Ibrahim.
He spoke to reporters after informing the families of the missing soldiers of the latest developments.
The families had gathered for hours in downtown Beirut amid blistering heat to await news of their loved ones.
They sat in tents they had pitched three years ago during protests to pressure the government to find the troops.
The army had said the missing soldiers were its "top concern", as it launched an offensive earlier this month against an estimated 600 IS jihadists in the border region.
Lebanese militant group Hezbollah, which had simultaneously launched its own assault against IS from the Syrian side of the border, also declared a ceasefire today.
Hezbollah's War Media channel said the unilateral pause was "in the framework of a comprehensive agreement to end the battle in west Qalamun against Daesh (IS)".
The deal is expected to see hundreds of IS fighters leave both sides of the border for an area in eastern Syria, Syrian and Lebanese sources said.
Mayadeen is an IS-held city near Syria's eastern border with Iraq.
The War Media channel said that 17 buses and 10 cars belonging to Syria's Red Crescent had arrived in the west Qalamun area in preparation for the evacuations.
Hezbollah has been fighting alongside troops loyal to President Bashar al-Assad since the Syrian conflict erupted in 2011.
Syria's state news agency SANA, quoting a military source, confirmed Hezbollah and IS had agreed that "the remaining Daesh (IS) fighters will leave to eastern Syria".
"When this happens, Daesh's military presence in Lebanon -- its control of geographic territory -- will be finished," the source said.
But the source warned that IS still had "sleeper cells" in Lebanon.
Six soldiers have been killed since the start of the assault, which the army has insisted is not being coordinated with Hezbollah.
Last month, Hezbollah carried out its own campaign further south on the border area against what is now Al- Qaeda's former affiliate, after Al-Nusra broke off ties with the extremist group last year.
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