President Cristina Kirchner stunned Argentina on Thursday by saying that a prosecutor who had accused her of a coverup had been killed, reversing her position that he had committed suicide.

The prosecutor, Alberto Nisman, was found dead with a bullet wound to his head a day before he was scheduled to testify in Congress that Mrs. Kirchner and her associates had conspired with Iran to sabotage a probe into a 1994 bombing that killed 85 people here.

“In Argentina, as in all places, not everything is what it appears to be, and vice versa,” Mrs. Kirchner said in a statement posted on her Facebook and Twitter accounts. “Why would he kill himself when he, as a prosecutor, and his family had an excellent quality of life?”

Mr. Nisman’s allegations, his death and the government’s reaction have shocked Argentines and sparked protests this week, with thousands of people carrying placards demanding justice. About 70% of Argentines believe Mr. Nisman was murdered, according to a poll released by Ipsos on Wednesday, and 82% found his allegations against government officials credible.

Alberto Nisman, the prosecutor who last week accused Argentine President Cristina Kirchner and others of working with Iran to cover up a 1994 terror bombing was found dead in his apartment on Sunday. Photo Associated Press

Mrs. Kirchner hasn’t spoken publicly about the incident, opting instead to issue two long letters that have added to the uncertainty.

“Why doesn’t she show her face and go on national television to talk about this?” said Juan González, a 33-year-old doctor. “Cristina said this was a suicide, and now she’s saying he was killed.”

Mrs. Kirchner raised a number of questions about Mr. Nisman’s death in her message.

She noted that he was the registered owner of two guns. Why, she asked, would he have shot himself with a .22-caliber handgun borrowed from an associate if he had two weapons that belonged to him?

Investigators have publicly said the weapon that killed Mr. Nisman belonged to an employee and close collaborator and that Mr. Nisman himself had purportedly asked to borrow the weapon on Saturday.

After Mr. Nisman’s death on Sunday, government officials quickly promoted the idea that the prosecutor had committed suicide, even before an autopsy had been completed. “Suicide prompts, in all cases, first stupor, then questions,” Mrs. Kirchner wrote in a letter on Monday that drew widespread criticism here.

An autopsy reported cited by Viviana Fein, the lead investigator on the case, said Mr. Nisman died of a self-inflicted gunshot wound fired at point-blank range into his temple. A gunpowder residue test later conducted on Mr. Nisman’s hands, however, turned out negative, she said.

Jorge Capitanich, Mrs. Kirchner’s cabinet chief, declined to discuss her reversal on Thursday, saying only that it was “clear, convincing” and spoke for itself.

Mrs. Kirchner’s about-face on the death may be the result of political calculation, said Victor Hugo Morales, a prominent radio personality close to the government. Mr. Morales said it may have been too costly for her to insist that Mr. Nisman had killed himself when few Argentines believed it.

Mrs. Kirchner leaves office in December and has struggled to find a candidate to carry on with her populist Peronist policies.

“For the government it was uncomfortable to continue supporting the idea that it was suicide,” Mr. Morales said on Thursday. “Politically, the government has little to lose in this sense to support the idea that it was a murder.”

Mr. Nisman, basing his allegations on intercepted telephone calls and other intelligence, had concluded in his 289-page complaint and in previous reports that top Iranian officials had used Hezbollah, the Lebanese Shiite group, to carry out a suicide bombing that killed 85 at the Argentine Israelite Mutual Association center, known here by its Spanish acronym AMIA.

Iran has denied any involvement in the bombing.

In conversations taped by intelligence agents that were revealed in his complaint, Mr. Nisman tried to recount how Argentine envoys spoke with Iran’s representatives here to forge a deal. In a May 2013 chat, Luis D’Elía, a prominent street activist who is a close ally of Mrs. Kirchner, called Jorge Khalil, identified as Iran’s local contact in Argentina, to tell him about government interest in furthering negotiations.

“They are willing to send people from [state oil company] YPF with us…to do business,” Mr. D’Elia said. He explained that there was interest in providing grains and beef for oil.

“YPF has not had any negotiations with Iran, nor has it bought or sold fuel with that country,” a YPF official said on Thursday.

Later that day, Mr. Khalil called Abdul Karim Paz, whom Mr. Nisman described as a Shiite Muslim religious leader and right-hand man to Mohsen Rabbani, Iran’s former cultural attaché in Buenos Aires, who is wanted for helping to orchestrate the 1994 bombing. “The issue is that Argentina needs oil,” Mr. Khalil told Mr. Karim Paz, according to the complaint. “Argentina has a big need for oil and Iran has a big need for grains.”

Mr. Khalil and Mr. D’Elía couldn’t be reached to comment, though Mr. D’Elia on Wednesday had said by phone that the allegations wouldn’t stand on their own merit. The whereabouts of Mr. Karim Paz and Mr. Rabbani, who left Argentina years ago, aren’t known.

In another taped conversation, Mr. D’Elia expressed hope that Iran would green light an Argentine plan for the truth commission—working together to resolve the bombing. In February 2013, Argentina’s Congress approved the plan.

Mr. Nisman said Argentina’s government saw a commission as an avenue toward justifying the opening of trade with Iran. “There is a green light to do the operations and to send the people,” Mr. Khalil, speaking for the Iranians, told Mr. D’Elia, in reference to moving forward on talks between the governments.

In addition to the alleged desire for Iranian oil, Mr. Nisman says that in 2012 Argentine leaders sensed that the global balance of power was shifting and that it would no longer be convenient for Argentina to “sustain its enmity toward Iran.”

To improve relations with the Persian country, Argentine authorities decided they needed to “definitively and fraudulently dissociate Iran” from responsibility for the 1994 bombing, according to Mr. Nisman’s complaint.