The former boxing champion described the Prince of Wales as “the greatest” in a letter read to him and the Duchess of Cornwall by Louisville's Mayor Greg Fischer.
Charles was visiting the Kentucky Centre for African American Heritage as part of a four-day tour of America when the message from Ali was read out.
“(My wife) Lonnie and I welcome you to our hometown of Louisville, Kentucky, USA,” Ali wrote.
"We are honoured that you have come to explore, share and learn about new sustainable initiatives that are so close to your heart.
Prince of Wales, tours the various exhibits on display at the Cultural Festival at the Kentucky Center for African American Heritage in Louisville "As you travel back to your homeland, we hope you know how much this city respects and admires the many contributions you have made in the world. We think you are the greatest."
The centre is close to the three-time heavyweight champion’s family home. Ali, who has Parkinson’s, has rarely been seen in public in recent months and was diagnosed with mild case of pneumonia in December.
Despite this, his family said he was still in good health and dismissed reports at the time that he was bedridden.
Read more: Muhammad Ali is not 'bedridden', say his daughters