A Filipino returning from Brazil tested positive for the P.1 variant after 752 samples were sequenced at the genome centre, the ministry said in a statement.
As many hospitals grapple with an acute shortage of oxygen and beds while morgues and crematoriums overflow, experts have said India's actual figures could be far higher than reported.
In Britain, where the rapid progression of the Delta variant has forced the government to delay its full reopening, thousands of anti-lockdown protesters meanwhile took to the streets of London to voice their frustration.
India's tally of infections stands at 406,130, the data showed, with the death toll rising by 374. On March 30, there were 354 deaths reported due to the pandemic.
Infections have been reported in more than 210 countries and territories since the first cases were identified in December 2019.
Li Qiang, an official in the city, the capital of central Hubei province, told a news briefing that "To ensure that everyone in the city is safe, city-wide nucleic acid testing will be quickly launched for all people to fully screen out positive results and asymptomatic infections."