The Hollywood heart throb, 60, was seen boarding a helicopter in Bari for an unknown destination on Tuesday, and is believed to be filming a scene in which he lands on an aircraft carrier.
The action hero arrived in the Puglia capital earlier this week.
Cruise, who is currently basking in the success of Top Gun: Maverick, is also a producer on this latest, and likely last outing for Ethan Hunt.
The Apulia Film Commission said it was not involved in the shoot but voiced satisfaction that American producers had once more chosen Puglia which "confirms it is a region in which there is everything you need for great cinema".
Mission: Impossible - Dead Reckoning Part Two is written and directed by Christopher McQuarrie, who is also producing it with Cruise.
The film is the eighth and final installment in the Mission: Impossible film series.
ANSA
