BOGOTA (Reuters) - Colombian former FARC guerrillas took their seats in Congress on Friday as part of an agreement that ended five decades of war, and outgoing President Juan Manuel Santos urged the nation to protect the nascent peace and put an end to violence.

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At the opening of the new Congress, one-time fighters for the Revolutionary Armed Forces of Colombia (FARC) filed into the lower house where they prepared to be sworn in collectively along with other members of the two chambers.

Under the terms of the 2016 peace deal between the FARC and the government, the group formed a political party, kept its famous acronym as the Revolutionary Alternative Common Force, and was awarded five seats each in the 108-member Senate and the 172-member lower house through 2026.

“Today we are witnessing a true milestone in our history,” said Santos, who won a Nobel Peace prize for his efforts to end the war, in his final address to Congress before leaving office on Aug. 7.

“Many - we must admit it - don’t like seeing them in this place of debate and civility,” Santos said. “In my case, and I’m sure it’s shared by millions of Colombians, it fills me with satisfaction that those who for more than half a century fought with arms against the state and its institutions, today submit to the Constitution and the laws of Colombia, as we all do.

“Welcome to this temple of democracy!”

Right-wing President-elect Ivan Duque will replace Santos next month and seek to guide key economic reforms - pension and tax - through the new Congress. He will also try and adjust the peace accords.

Duque and his Democratic Center party want to scrap an amnesty for FARC commanders who committed crimes, including engagement in the cocaine trafficking that helped bankroll the group, and prevent them from participating in politics until they serve out prison sentences.

Duque, a 41-year-old protege of former President Alvaro Uribe, whose hard-line battle offensive against the rebels helped push them to the negotiating table, has said he is incensed there would be “criminals” in Congress shaping laws after decades of kidnapping, extortion and killing.

He said he would alter the peace accord by forging alliances in Congress, where his party holds just 51 of 280 seats, and by generating a national consensus.

The FARC’s presence in Congress promises to create tension. Uribe, whose hatred for the rebels was born after his father was killed in a botched kidnapping, has a seat in the Senate.

He and his party will likely seek to block votes on initiatives put forward by the FARC for having participated in a conflict that left 220,000 dead and millions displaced.

But while Duque may make minor changes to the peace accord, it would be almost impossible for him to make substantive alterations to something backed by about three-quarters of Congress, analysts have said.

The left parties have said they will join forces to seek to block any changes.

“We want to build a democratic, intelligent and collective opposition with aspirations to govern,” Angela Maria Robledo, a lower house lawmaker from the leftist coalition of parties, told reporters.

Leftwing Gustavo Petro, Duque’s rival in the presidential race, will lead the opposition in the Senate.