The Dutchman, whose opinions hold considerable sway at the club, said his relative lack of experience at the helm of a club also counts against his ability to lead Barca in the short-term.
Vilanova only took over from Pep Guardiola in the summer. He led the club to the Liga title and semi-finals of the Champions League despite spending three months away from the team to recover from parotid gland cancer surgery for a second time in New York.
"Tito has not got as much experience as Pep Guardiola and also has a huge problem - his illness,” Cruyff, who was boss at the Catalan giants for eight years, winning four titles, the club's first European Cup in 1992, a Cup Winners' Cup and Copa del Rey, told Catalunya Radio.
“It is not advisable to coach when you are still trying to get back your strength. I had heart surgery but can you coach Barcelona when you are not 100 per cent?
"First of all I would advise Tito to take care.”
Asked whether Barca should have appointed a temporary coach last season instead of leaving assistant Jordi Roura in charge, Cruyff was unequivocal.
“I think so. Sometimes you need to make decisions even though they are very difficult. Everyone must think about the team," he said.
“If the team is to function then everyone has to think more of the team than themselves."
Cruyff added that he is surprised goalkeeper Victor Valdes is leaving the club.
“It is a strange thing that Victor Valdes wants to leave the best club in the world,” he said.