The Mission Impossible star was honoured by Tanaiste and Foreign Affairs Minister Eamon Gilmore, after researchers discovered one of his ancestors restored evicted tenants to lands just before the famine.
The research discovered the actor's great-great-great grandfather, Patrick Russell Cruise, returned from America to Ireland after his land agent forced families from farms in Co Westmeath in 1843.
The landlord restored tenants to 500 acres around the townlands in Paristown and Dardistown in the years before the Great Famine when potato crops repeatedly failed.
After the certificate presentation at Iveagh House in Dublin, Cruise said he had been taken aback by the extent of his ancestry.
"To learn about the history of my family - it was incredible," he said.
"I knew I was Irish but I had no idea where it went and the depth of it. It goes all the way back to the 12th century."
Cruise was born Tom Cruise Mapathor IV in 1962.
I knew I was Irish but I had no idea where it went and the depth of it.
The research was commissioned by Tourism Ireland on behalf of The Gathering - an initiative to attract the Irish diaspora to visit Ireland through 2013.
It revealed that the Cruise and Mapathor families had settled in Ireland, with roots going back 800 years.
A third family, the Russells, were also prominent in Cruise's ancestry.
Tourism Ireland claimed Cruise's ancestry includes knights, rebels and the "hero landlord".
Cruise was in Dublin for the premiere of his latest blockbuster Oblivion, as well as engagements with the Irish Film Board, a pre-recorded Late Late Show interview and a visit to the Guinness brewery.
The star added: "It's a great honour for me and for my whole family - I can't wait to bring it back to them and enlighten them on their history.
"I'm very proud to be Irish. There's a pride in America of being Irish. I can't wait to come back and I want to visit the land of my ancestors and the castle that they had."