Mr. Macri’s coalition, currently a minority in Congress, was expected to pick up several seats on Sunday, a showing that would strengthen the president’s hand in pursuing an ambitious economic program that is unpopular among many Argentines.
The Maldonado case became a thorn in the ruling party’s campaign, and the latest twist could raise questions in voters’ minds about the government’s handling of the investigation.
The most widely watched race is in Buenos Aires Province, where a candidate from Mr. Macri’s coalition faces the president’s predecessor, and most prominent political antagonist, former President Cristina Fernández de Kirchner.
The discovery of the corpse was a dramatic turning point in a case that has dominated headlines in Argentina for weeks, evoking painful memories of abductions, mass disappearances and killings during the country’s 1976-1983 military dictatorship.
Mr. Maldonado’s relatives, human rights activists and much of the opposition have harshly criticized the government for quickly coming to the defense of the security forces who evicted the indigenous rights protesters.
Officials, including the security minister, Patricia Bullrich, openly questioned whether Mr. Maldonado was even at the protest. Elisa Carrió, the lawmaker who heads the government coalition’s ticket in the city of Buenos Aires for Sunday’s election, said last week in a televised debate that there was a “20 percent chance” Mr. Maldonado was in Chile. She later apologized.
“We don’t trust anyone,” said Andrea Antico, Mr. Maldonado’s sister-in-law, explaining why she and her husband spent several hours watching the corpse floating in the Chubut River until forensic experts could arrive.
The recovery of the body near where Mr. Maldonado had vanished, in an area the family says had already been scoured three times, raised new questions about the investigation. The case has spurred nationwide protests and a social media phenomenon as many Argentines posted Twitter and Facebook messages asking: “Where is Santiago Maldonado?”
Mr. Maldonado’s family said they suspected the body had been planted, pointing out that it was upriver from where he was last seen. “I can’t assure it, but I think it was” planted, Sergio Maldonado said.
Mr. Maldonado had taken part in a protest in Chubut Province by members of the Mapuche indigenous community, which has long claimed rights to part of territory owned by Benetton, the Italian clothing company.
“This is not the end that we would have preferred,” María Eugenia Vidal, the governor of Buenos Aires Province and a close ally of Mr. Macri, said in a radio interview today, referring to the election campaign. “Besides, there is still very little clarity as we wait for the result of the tests that will determine if the body is Santiago’s.”
Neither Mr. Macri nor Mrs. Kirchner have commented on the discovery of the body. “Macri’s silence could end up hurting him, particularly when much of the population has always doubted his commitment to human rights issues,” the analyst Mariel Fornoni said.
Mr. Macri’s government has said it was giving investigators a chance to do their job. “The president has been following everything with concern and gave us the order to put everything at the disposal of the courts so it can be cleared up as quickly as possible,” Germán Garavano, the justice and human rights minister, told the state-run news agency Télam.
Others have criticized the government. Officials’ first reaction “was to protect the border guards” who broke up the Aug. 1 protest, said Sergio Massa, a candidate in the Buenos Aires senate race.
In the weeks before the election, Mrs. Kirchner accused Mr. Macri’s government of trying to distract from the disappearance of Mr. Maldonado by pushing numerous judicial cases against her and her allies.
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