The investigation is focused on the alleged failure to promptly seal off two towns in Lombardy — Alzano Lombardo and Nembro — where a major coronavirus outbreak was identified.
The northern region of Lombardy has been ground zero for Italy, with about 16,000 deaths so far during the pandemic, almost half of the nation’s total.
Locals say that almost every family in the towns is grieving a lost relative.
Conte told Italian media he was "not worried" about the probe and had followed “conscience and science.”
Relatives of virus victims protested this week in Bergamo, the capital of the province, filing 50 criminal complaints and demanding an investigation to bring those responsible to justice.
The Lombardy regional government has blamed Rome for the alleged failure to promptly extend the virus containment area, known as the red zone, in late February.
The government’s scientific and technical committee had suggested that the area be included in the red zone after the number of coronavirus infections surged to 80 in early March.
But the final decision to isolate the area was delayed, until the entire region of Lombardy, and then Italy as a whole went into lockdown on March 10.
Conte has insisted that the Lombardy government had the power to close the area, as other regions did.
A team of four prosecutors from Bergamo questioned Conte on Friday at his Palazzo Chigi offices in Rome for about three hours. Conte is not believed to be a suspect.
They were later set to question the health and interior ministers, Roberto Speranza and Luciana Lamorgese.