The country announced a sharp increase in deaths from 69,342 to 180,764 since the pandemic began, according to Johns Hopkins University data.
Health Minister Oscar Ugarte said the criteria for identifying coronavirus as a cause of death had been changed.
Previously, only those who "had a positive diagnostic test" were considered to have died from the virus, but other criteria have since been incorporated.
Countries across the world are seeing a surge in coronavirus cases and deaths.
Peru is one of three countries, along with the US and Brazil, to report a 24-hour tally of Covid-19 deaths that exceeded 4,000 this week.
Meanwhile India hit a peak of almost 127,000 new cases in 24 hours, and Iran set a new Covid infection record for the third straight day, reporting nearly 22,600 new cases.
Questions about Peru's death toll surfaced soon after the beginning of the pandemic.
The latest figures were announced in the presidential palace during the presentation of a report to analyse and update the death toll.
Among Latin American countries, only Brazil and Mexico have reported higher death tolls from the disease.
Prime Minister Violeta Bermudez reassured that support continues for Peru with “hope and confidence.”
“The vaccination process continues throughout the country,” she said in a tweet on May 29.
“Today in Lima and Callao we are monitoring the progress in Surco, San Martín de Porres and Carmen de la Legua.
“Let's continue to lend a hand for Peru with #confidence and hope.”
At least 3,694,005 doses of Covid vaccines have been administered in Peru so far, according to Reuters.
Assuming every person needs two doses, that’s enough to have vaccinated about 5.7% of the country’s population.
