Scott, 68, jumped to his death from the Vincent Thomas Bridge on Sunday.
"Tony was my dear friend and I will really miss him. My deepest sorrow and thoughts are with his family at this time," Cruise, 50 said.
The actor, who teamed up with the director on 'Top Gun' and 'Days of Thunder', described Scott as "a creative visionary whose mark on film is immeasurable".
The actor-director were reportedly planning to team up again for a sequel of 'Top Gun. They were in Nevada late last week touring a Naval air station as part of their research for the movie, the Hollywood Reporter said.
'Top Gun 2' was one of three directing projects on Scott's plate that were in advanced development before the director killed himself.
Meanwhile, conflicting reports are emerging about inoperable brain cancer that could have prompted the suicide.
LA County chief coroner investigator Craig Harvey said that Scott's family has disputed the report that he had inoperable brain cancer.
