Kuyt was left out of a 21-man squad named yesterday for next week's friendly against Croatia.
Van Basten said: "The system we had can be compared with Liverpool's - and his performances are not good enough."
Kuyt, 27, made his debut under Van Basten in 2004 and won 35 caps.
But he has only seven goals this term and has not scored in 11 games.
Kop team-mate Ryan Babel makes the squad.