"Tony was my dear friend and I will really miss him," contactmusic.com quoted Cruise as saying.
Scott directed Cruise in 1986 "Top Gun" and in 1990 release "Days of Thunder".
Cruise said his mark on the film industry cannot be measured.
"He was a creative visionary whose mark on film is immeasurable. My deepest sorrow and thoughts are with his family at this time."
Scott, 68, committed suicide Sunday afternoon. He is survived by his wife, Donna, and two sons.