"The current government will have the historic responsibility to continue with the full implementation of the peace agreement," Alberto Brunori, the UN's human rights chief in Colombia, said in a speech in Bogota.
Duque was elected last year on a pledge to roll back some aspects of the deal that ended five decades of conflict in the South American country.
He announced plans last week to reform the Special Jurisdiction for Peace (JEP), set up under the agreement to try former combatants accused of atrocities.
The right-wing president has announced that he will object before Congress to six of the 159 articles of the law that regulates the JEP, considered the backbone of the peace pact negotiated in Havana.
Under the JEP, ex-rebels or soldiers would receive alternative sentences to prison time if they confess their crimes, compensate victims and pledge never to resort to violence again.
Negotiators of the 2016 peace pact have warned the United Nations that the move would "seriously damage" the accord.
"The construction of a stable and lasting peace depends on the urgent approval and promulgation without denunciations of the draft statute law of the Special Jurisdiction for Peace," said Brunori, who was presenting the annual human rights report for Colombia.
Transformed into a political party since the peace deal, FARC has hit out repeatedly at the lack of security guarantees for its members.
While some 7,000 ex-fighters laid down their weapons, Colombia's peace and reconciliation commission estimates 1,600 dissident rebels remain active.
The UN office has also described as "worrying" the human rights situation in Colombia, including the killings of activists and community leaders.
Some cases are linked to "substantial delays in the implementation" of the peace agreement, according to the UN. Brunori reported 113 killings in 2018 alone.