The investigation, which could put Bolsonaro on trial or even impeached, comes as his popularity dips because of his handling of the coronavirus outbreak that has claimed more than 20,000 lives in Brazil and is now the third most affected country with more than 310,000 cases.
Brazil - now home to the third-highest number of cases in the world after the United States and Russian Federation - has recorded more than 20,000 deaths and hit a record 24-hour toll of 1,188.
Interim Health Minister Eduardo Pazuello, an active-duty army general, authorized the modified protocol to promote the use of chloroquine and hydroxychloroquine.
President Jair Bolsonaro is under growing pressure for his handling of the outbreak, which looks set to destroy the Brazilian economy and threatens his re-election hopes.
A Brazilian Supreme Court judge ruled Friday to release a video that allegedly shows President Jair Bolsonaro trying to interfere with a law enforcement probe in order to protect his son from being investigated.
Like US President Donald Trump, to whom he is often compared, Bolsonaro has hailed chloroquine as a potential wonder drug against the novel coronavirus, even though some studies have cast doubt on its effectiveness and safety.
In researches conducted the month prior, analysis have shown that use of the drug in US hospitals for veterans raised no significant or definitive changes.
Sao Paulo, the most populous city in the country, has recorded 5,363 deaths, which is more than China, where the disease outbreak began in December.
On Monday, São Paulo Mayor Bruno Covas said that the city's public hospitals had reached 90 percent capacity and that in only two weeks they will no longer be able to support the influx of patients. "It has no scientific evidence", Vecina Neto said, "It's unbelievable that in the 21st century, we are living off magical thinking". "We're sending them ventilators", Trump tells reporters during a cabinet meeting at the White House. "Brazil is having some trouble, no question about it".
"I don't want people over there sick, either", Trump added.
Guided by the head of state, the Ministry of Health published a new protocol on the treatment of patients with coronavirus, which extends the possible use of chloroquine and hydroxychloroquine in mild cases, Despite the fact that the efficacy of these antimalarials has not yet been demonstrated in the fight against the virus.
India to 'gradually' restart rail operations in lockdown easing
Also, only COVID 19 asymptomatic passengers will be allowed to board these trains. Every Shramik special train has 24 coaches, each with a capacity of 72 seats.