RIO DE JANEIRO, June 29 (Reuters) - Brazil will suspend a $324 million Indian COVID-19 vaccine contract that has mired President Jair Bolsonaro in accusations of irregularities, the health minister said on Tuesday, following the guidance of the federal comptroller, the CGU. The deal to buy 20 million doses of Bharat Biotech"s Covaxin shot has become a headache for Bolsonaro after whistleblowers went public with alleged irregularities. One Health Ministry official said he alerted the president about his concerns. Bolsonaro, whose popularity has faded as Brazil"s COVID-19 death toll climbed past 500,000, has denied any wrongdoing, saying on Monday he was not aware of any irregularities. But thorny questions refuse to go away, and may pose problems for him ahead of next year"s presidential vote. Brazil Health Minister Marcelo Queiroga said at a news conference his team would probe the allegations during the suspension. "According to the preliminary analysis of the CGU, there are no irregularities in the contract but, for compliance, the Health Ministry chose to suspend the contract," the ministry said in a statement. Earlier on Thursday, CNN Brasil reported that the ministry had decided to cancel the contract. Brazilian federal prosecutors have opened an investigation into the deal, citing comparatively high prices, quick talks and pending regulatory approvals as red flags. It is also being probed by a Senate panel investigating the government"s handling of the pandemic. One of the leading opposition senators on that panel filed a formal criminal complaint against Bolsonaro at the Supreme Court on Monday. Senator Randolfe Rodrigues said he wanted the court to investigate "the serious allegations" and to find out why Bolsonaro "did not take any action after being notified of the existence of a giant corruption scheme in the Health Ministry." ($1 = 4.9403 reais)