The Chelsea forward completed the full 90 minutes as Belgium lost out to France on Thursday night, the 28-year-old making his 11th appearance of the season.
However, rather than face the European champions on Sunday, Lukaku has left his nation's training camp due to "muscle overload".
Speaking to reporters, Martinez said: "It's an overload. He didn't feel 100% to play tomorrow. It's soreness in his tissue. Every decision taken involves both medical departments together for the good of the player.
"[Eden] Hazard and Lukaku are in similar physical condition; they had a muscle overload and we don't have the facilities to do the usual medical work.
"They will return to Belgium to get back to their best shape for the clubs. Obviously there's an excellent understanding between the two medical staff and we want to do what's best for the player."
Chelsea are not back in action until they square off against Brentford in the Premier League on October 16. body check tags ::