Thousands of protesters across Brazil demonstrated against President Jair Bolsonaro this weekend as pressure mounted on the populist leader over allegations of potential corruption in the procurement of Covid-19 vaccines.

The rallies, which took place in at least 13 state capital cities, came a day after the Supreme Court authorised a criminal investigation into whether Bolsonaro engaged in the crime of “prevarication”, the dereliction of public duty for reasons of personal interest.

Bolsonaro has been accused of not acting on suspicions of wrongdoing after a whistleblower at the Ministry of Health claimed to have personally raised with him concerns about a R$1.6bn ($320m) deal to acquire 20m jabs of Covaxin produced by Bharat Biotech from India.

The scandal came to the fore after Luis Ricardo Miranda, chief of the ministry’s import division, highlighted alleged irregularities in invoices. The civil servant said he was pressured by a senior government official to push through the orders.

Miranda and his brother, a federal deputy, last month testified to a congressional inquiry that they had brought the issue to the Brazilian president, and that he gave assurances he would raise the matter with police. Federal police, however, say they did not receive any request to investigate.

Ministers have denied irregularities in the Covaxin agreement, which involved an intermediary company, while insisting that no money has been paid since no batches of the shots have yet been delivered. Bolsonaro and Bharat have previously denied wrongdoing in the supply of Covaxin. The health ministry temporarily suspended the contract after a recommendation from the federal comptroller.

With more than half a million lives lost to Covid-19 in Latin America’s most populous nation, the controversy has become a political headache for the Bolsonaro administration. The return of protesters to the streets of Brazil’s big cities raises the pressure on the president ahead of his re-election campaign next year.

Many claim the populist leader, who has railed against lockdowns and disparaged the use of masks, has been negligent in his handling of the pandemic.

“The ‘silent’ majority that opposes the president has started to hit the streets, led by the left but with growing support from centrist voters. The wheels are forcefully turning against the president,” said Mario Marconini, managing director of Teneo in Brazil.

Political analysts, however, are sceptical about the potential impact of the probe. Any criminal charges brought against the president would need to garner the backing of two-thirds of the lower house of Congress in order to proceed, an unlikely outcome given Bolsonaro’s web of alliances in parliament.

“If the attorney-general, nominated by Bolsonaro, decides there is enough evidence to indict him, the Supreme Court will need approval from the lower house to move forward and house speaker Arthur Lira can just do nothing,” said Eduardo Mello, a political scientist at the Getúlio Vargas Foundation, highlighting Bolsonaro’s alliance with Lira.

A grouping of left- and rightwing deputies last week filed a new request for impeachment but for now the prospects appear slim. The leader of the lower house of Congress, Lira, who must approve any request, has until now given no indication he is minded to start proceedings.

“Bolsonaro still maintains 25 per cent approval in the polls and his allies in parliament are in a comfortable position,” said Lucas de Aragão, a partner at consultancy Arko Advice. “This scandal is damaging but not necessarily fatal.”