Cameroon crashed out 3-2 to Nigeria last Saturday, an exit the federation described as "premature" in its statement.
Former Dutch international Seedorf won just three of nine competitive games after taking over the Indomitable Lions alongside Kluivert last August.
The federation are now hunting for a manager to prepare the national side for the 2021 Africa Cup of Nations which they are hosting.
With a haul of four Champions League wins, five national titles and a host of individuals awards, Seedorf, a former AC Milan and Real Madrid midfielder enjoyed a decorated career on the pitch.
But his transition into management has come with a steep learning curve.
Failures with Milan and Chinese club Shenzhen, relegation with Deportivo La Coruna and early elimination with Cameroon have clouded his reputation.