The on-loan Manchester City striker lasted only 45 minutes of Saturday's goalless draw with Newcastle before a recurrence of a groin problem.
Kean told BBC Radio Lancashire: "His concerns in the past have been other injuries.
"Because he hasn't played as many minutes at City he might pick up another little niggle here and there."
Kean continued: "It's only a small injury, and we've got a break now until our next game at Villa to get some extensive treatment on it and do some tough work with him in the gym, and on the training ground, and hopefully he'll be 100% fit."
Santa Cruz has completed ninety minutes just once in four games since he returned to Ewood Park in January for the remainder of the season.
Kean added: "The doctor said that Roque could only sprint at 75-80%."
"The last thing you want is him missing three or four games, so he was brought off as a precaution.
Rovers also expect winger Junior Hoilett to be fit to face Villa on 26 February.
Source: BBC Sport
Source: BBC Sport