The 22-year-old joined the Spanish champions in the close-season from Santos, with the financial arrangements surrounding his transfer causing controversy in recent months.
Sandro Rosell resigned as president over the affair, although the club denied any wrongdoing after being charged with tax evasion by the Spanish authorities.
And Cruyff, who played 227 times for Barca between 1973 and 1978, feels the off-field issues relating to the Brazilian's move are proving troublesome.
"At Barca and at any big team, the coach has to be the boss. That's why Pep (Guardiola) left, because the board interfered. And Barca's problem is Neymar," he said in quotes reported by AS.
"He's a terrific player, there can be no argument about that, but you can't sign a 21-year-old player and pay him a higher wage than players who have won everything."
By Barca's own standards, their campaign has been somewhat disappointing, losing four times in the league to sit a point behind Madrid neighbours Real and Atletico.
However, Lionel Messi's hat-trick helped keep their title hopes alive with victory in El Clasico on Sunday and Cruyff feels the Argentina international, rather than Neymar, remains the key figure for Gerardo Martino.
"If you already have the best player in the world, a 21-year-old player (Neymar) can't be the main man," Cruyff added.
"That's impossible in football. At 26 he can, but at 21 it's impossible."
