The departure of Jaime Manalich was announced by President Sebastian Pinera.
The government has said publicly that the health crisis has claimed more than 3,000 lives since the first case emerged in Chile on March 3.
A report Saturday, however, revealed that Chile had informed the World Health Organization (WHO) that the death toll was actually more than 5,000.
The report came from an investigative journalism organization called CIPER which obtained a copy of the health ministry documents sent to the WHO.
Manalich had faced mounting criticism over the way the health ministry tallies COVID-19 deaths.
Deputy Health Minister Paula Daza explained the difference in the numbers.
She said the higher figure presented to WHO includes both confirmed and suspected COVID-19 deaths, while the government’s daily report reflects only those cases confirmed by a test based on a nasal swab.
On Friday, Chile reported a record for new infections and deaths over a 24-hour period — 6,754 and 222, respectively.
“The situation in our country continues to rise, above all in the metropolitan region,” health ministry official Arturo Zuniga said Friday.
Infections have risen steadily in Chile even though it began taking emergency measures in February — including widespread testing and the closure of borders and schools — making it one of the first Latin American countries to do so.
The capital Santiago and its seven million people were placed on lockdown more than a month ago; they were joined on Friday by the cities of Valparaiso and Vina del Mar.
Nearly half of Chile’s population of 18 million is now under strict confinement.
The country initially had imposed selective quarantines on areas with high incidence of the coronavirus.
But many poorer Chileans continued going to work — out of economic necessity — and a sharp resurgence in mid-May forced the government to order a strict lockdown.