The sudden departure of the military leaders came a day after President Jair Bolsonaro fired his defense minister and reshaped his cabinet.

By Ernesto Londoño

RIO DE JANEIRO — The three commanders of Brazil’s Armed Forces resigned jointly on Tuesday, a day after President Jair Bolsonaro fired his defense minister as part of a big cabinet shake-up.

The departures of the military leaders, which followed the unexpected replacement on Monday of five other cabinet members fueled rampant speculation in the capital about a breakdown in the relationship between the president and the country’s military, which has played a central role in the Bolsonaro administration.

“The dismissal of the heads of the Army, the Navy and the Air Force after the sudden shift in leadership at the defense ministry is unprecedented in the era since democracy was restored,” Representative Rodrigo de Castro said in a statement. “It reveals a real crisis between the military and the government.”

The political turbulence in Brasília comes as the government faces withering criticism at home and abroad for its handling of the Covid-19 pandemic, including calls for Mr. Bolsonaro’s impeachment. A surge in infections has overwhelmed hospitals across the country, leaving patients to die waiting for a hospital bed.

Mr. Bolsonaro, a former Army captain, has given the military a leading role in politics and policymaking in Brazil, entrusting its leaders with the most power they have had since the country’s military dictatorship ended three decades ago. He picked a retired Army general as a running mate and appointed top military leaders for scores of leadership roles that are normally occupied by civilians.
But military leaders have failed at core missions Mr. Bolsonaro gave them, including overseeing the response to the pandemic and reining in deforestation in the Amazon.

The president’s relationship with his vice president, retired Gen. Hamilton Mourão, and his departing defense minister, Gen. Fernando Azevedo e Silva, grew tense in recent weeks as the country’s coronavirus crisis worsened.

Last week the president replaced his health minister, Eduardo Pazuello, an active duty general who failed to lead a comprehensive response to the pandemic and to negotiate the purchase of a sufficient amount of Covid-19 vaccine.

The Brazilian government’s response to the pandemic, which has killed more than 313,000 Brazilians, has been cavalier and chaotic.

In his resignation letter, Gen. Azevedo e Silva said he had sought to “preserve the armed forces as an institution of the state.” The phrase appeared to convey a belief that Mr. Bolsonaro had sought to politicize the armed forces.

The resignation of the three military commanders — Gen. Edson Pujol of the Army; Lt. Gen. Antonio Carlos Moretti Bermudez of the Air Force; and Adm. Ilques Barbosa Junior of the Navy — was announced in a short statement issued by the defense ministry. It did not provide a reason.

Monday’s cabinet changes included the departure of the foreign minister, Ernesto Araújo, a hard-line conservative who picked fights with the government of China, Brazil’s top trading partner and the principal purveyor of the vaccines currently available to Brazil.

Lawmakers criticized the departing top diplomat for the country’s failure to secure access to a large number of Covid-19 vaccines.

Mr. Bolsonaro also replaced his justice minister, his chief of staff and the lawyer who represents the executive branch in cases before the Supreme Court.

Mr. Bolsonaro did not provide an explanation for these changes and analysts were struggling on Tuesday to make sense of their implications.

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