They are Sports Minister George Hilton and Col. Adilson Moreira, who was organizing security at the Olympic Games in Rio de Janeiro in August.
Col. Adilson Moreira reportedly wrote that he was ashamed Brazil was being led by “an unscrupulous group”.
The resignations come as President Dilma Rousseff battles for her government’s survival in an impeachment process.
Col. Adilson Moreira led the National Force for Public Security, whose members will guard sporting venues during the Olympics.
Brazilian media reported the colonel had sent an email to his colleagues criticizing President Dilma Rousseff and other senior officials.
Brazilian officials said the planning for the Olympic Games would not be affected by Col. Adilson Moreira’s and George Hilton’s resignations.
Dilma Rousseff’s supporters marched on March 31 in a number of Brazilian cities to show their opposition to the impeachment proceedings.
On March 28, Tourism Minister Henrique Eduardo Alves handed in his letter of resignation, pre-empting his PMDB party’s split from the governing coalition.
The PMDB was the largest partner in the governing coalition and its exit could deprive Dilma Rousseff of crucial votes she needs to block impeachment proceedings against her.
Dilma Rousseff is expected to announce sweeping changes to her cabinet on April 1 to replace up to seven ministers from the PMDB party.
The president’s critics say she is trying to buy the votes of smaller parties by offering them posts in the cabinet.
Congress is expected to start voting next month on whether to remove Dilma Rousseff from office over allegations that she manipulated accounts to hide a growing deficit.
If 172 out of the 513 members of the lower house of Congress vote against Dilma Rousseff’s impeachment, the proceedings will be shelved.
However, if 342 members vote for it, President Dilma Rousseff will be suspended for 180 days and Vice-President Michel Temer of the PMDB party will become interim president.
The impeachment would then by reviewed by the upper house, the Senate, and a final decision be taken in October.
Dilma Rousseff has denied any wrongdoing and has likened the moves to impeach her to an attempted coup.
Separately, ex-President Luiz Inacio Lula da Silva continues to be investigated as part of a corruption case involving the state-run oil company Petrobras.
On March 31, Luiz Inacio Lula da Silva was handed a boost as Brazil’s Supreme Court ruled it would take over the case.
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