President Jimmy Morales sparked an international outcry in January when he announced he would not renew the mandate of the UN-backed International Commission Against Impunity in Guatemala.
The body, known by its Spanish acronym CICIG, has been in the eye of the storm since it began investigating Morales' own family for corruption.
"Guatemalans are witnessing the exit of CICIG, which is due to pressure from people from dark sectors," said Eleonora Muralles, head of a victims' group.
"It investigated those powers that were previously hidden and now are unmasked, belonging to economic elites that were untouchable here.
"Now they want to reverse the work so that there be no more investigations," said Muralles, president of the association of Families and Friends against Crime and Kidnapping.
Alvaro Montenegro, a member of the Alliance for Reforms collective, said CICIG "touched the heart of impunity and corruption" in Guatemala, by targeting "characters who have very strong economic power."
CICIG was set up in 2007 to investigate organized crime groups, which have gained influence since the end of the country's armed conflict in the 1990s.
- 'Decisive contribution -
==========================
UN chief Antonio Guterres paid tribute in a statement Tuesday, saying it "made a decisive contribution to strengthen the rule of law as well as investigation and prosecution capacities in Guatemala."
In its final report, CICIG said it had dismantled 70 criminal structures, brought 600 people to trial and obtained 400 convictions since it began operations in 2007.
In its most high-profile case, charges were filed in 2015 against former president Otto Perez Molina and his wife Roxana Baldetti in a massive customs corruption scandal known as La Linea.
Baldetti was jailed for 15 years in 2018 while Perez remains in pre-trial detention.
Another former president, Alvaro Colom, was arrested in February over allegations related to graft in the public transport system.
His ex-wife Sandra Torres, defeated in last month's presidential elections, was placed under investigation Monday as part of a probe dating back to 2015.
President-elect Alejandro Giammattei, who will replace Morales in January, has said CICIG will be replaced by a government anti-corruption commission with international funding.
Morales in January said the UN-backed body had become "a threat to peace" in Guatemala.
"CICIG gave us good experiences and ones that were not so good," Giammattei said Tuesday.
"But they left us something, and that is the need to fight together for the reconstruction of our institutions."
Avoiding a setback in the anti-corruption fight in the wake of CICIG's departure "will be a big challenge," said Montenegro.
"Citizens will have to take on the responsibility of pushing the Public Ministry for action. To be watching, supervising and demanding that this work be continued," Montenegro told AFP.
The Right Livelihood Foundation's chief Ole von Uexkull said CICIG's model "should be used as a roadmap for the future in other parts of the world where corruption is damaging society."