The 66-year-old is unsure whether or not the duo will initially combine to devastating effect as has been forecast for them by stating it may take a couple of years
The 21-year-old made his long-awaited debut for the Blaugrana recently following his €57 million move from Santos earlier in the summer, but is yet to start a game alongside the Argentine in preseason.
Cryuff, who enjoyed a five-year stint with the Catalans as a player, admits both are "geniuses" but believes the world may not see the best of them in tandem for a couple of years.
He told Peru-based publication The Trade: "They are both geniuses, but first we must see how they play with each other and with the rest of the team. Two captains on a ship could bring problems.
"If the board makes a decision it must be respected, but I'm just making an observation that it may have been better to wait a few more years before putting them together.
"I had hoped to see them together when Messi was a little older and see how it worked. Neymar has many qualities as a player, but at 21 he is not fully developed yet."
The former Netherlands international, who coached the Spanish giants for eight years until 1996, went on to criticize the current board at Camp Nou for what he believes was a knee-jerk appointment of new coach Gerardo Martino.
"As Tito was sick, everything was done in a hurry. It was an appointment done without preparation and the decision was made in a hurry," Cruyff said.
When asked who his best "student" was throughout his eight-year stay in Catalunya, the 66-year-old named Bayern Munich boss Pep Guardiola, who "sees the game as God intended" and Frank Rijkaard, a former Barca player and coach.
"I would say my best student was Pep, especially because he is now at a very high level - and then Rijkaard," he continued.
"Pep has done things very similar to what I did when I was a coach, not just for style but also the type of club he has coached.
"He is a great coach, very smart, see things as God intended."