The commission has helped Guatemala’s attorney general’s office pursue vigorous anti-corruption prosecutions. Under Mr. Velásquez, it uncovered a customs fraud scheme that prosecutors say was led by President Otto Pérez Molina, who resigned shortly before the end of his term in 2015 and has been in jail ever since.
Mr. Rubio’s action was prompted by the case of a Russian family convicted in January of buying false passports in Guatemala and sentenced to long prison terms. The Bitkov family, who fled Russia in 2009, say they were seeking a safe haven after their successful paper business was raided by Russian banks that called in hundreds of millions of dollars in loans.
“I am concerned that Cicig, a commission mostly funded by the United States, has been manipulated and used by radical elements and Russia’s campaign against the Bitkov family in Guatemala,” Mr. Rubio said in a statement, using the Spanish initials for the commission.
“Cicig was established by the United Nations and Guatemala to prosecute official corruption and human rights abuses, not to participate in it,” Mr. Rubio said, adding that the hold on the funding would stay in place “until we have clear answers on its role in the mistreatment of the Bitkov family.”
Mr. Rubio did not specify what action was needed to lift the hold.
Last week, Guatemala’s highest court threw out the family’s convictions and sent their case back to the trial judge, with orders to reconsider their case. They could be released from jail this week.
The United Nations commission “has been doing terrific work on a whole host of issues with the attorney general of Guatemala,” said Eric Olson, a Guatemala expert with the Wilson Center in Washington. “It would be unfortunate if this led to some irreparable harm to those efforts.”
Senator Patrick J. Leahy, a Vermont Democrat who has supported the commission, warned against using the Bitkov case to attack it. “If Mr. Velasquez is removed for specious reasons or Cicig is shut down, it would set back the cause of justice and seriously jeopardize U.S. assistance to the government of Guatemala,” he said on Sunday.
The family’s plight caught the attention of William F. Browder, a prominent investor who has led an international campaign to punish Russian human rights abusers. After a Guatemalan court sentenced Igor Bitkov to 19 years in jail, and his wife, Irina, and daughter, Anastasia, to 14 years for using false documents, Mr. Browder began working to free the family. He made Mr. Velásquez and the commission one of his targets.
Mr. Browder argues that the Russian government, through the state-owned bank VTB, pushed for the commission and the Guatemalan attorney general’s office to wrap the Bitkovs into a longstanding investigation into a scheme at the government’s passport office to sell fake passports.
“All of these people who are screaming about the sacred cow of the Cicig are doing an injustice to the Cicig because the Cicig is clearly involved with the Russians in a vendetta against the Bitkov family,” Mr. Browder said in a telephone interview on Sunday.
Cicig said it had identified the Bitkovs’ purchase of the passports independently.
Despite widespread support for the commission in Congress and among members of the Trump administration, Mr. Browder’s zeal for the Bitkovs’ case struck a chord with Mr. Rubio.
Three Republican lawmakers — Senators Roger F. Wicker of Mississippi and Mike Lee of Utah, and Representative Christopher H. Smith of New Jersey — joined Mr. Rubio in writing to the chairmen of the House and Senate committees on foreign relations to suspend funding to the commission.
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