Complex sentence: The system only applies to players currently under contract with a Japanese team; it does not apply to free agents, players who have ten or more years of playing service with NPB or amateur players who have never played in NPB.
Split into simpler sentences: The system only applies to players currently under contract with a Japanese team, although players who have ten or more years of playing service with NPB are exempt. It does not apply to free agents, or to amateur players who have never played in NPB.