Oita Trinita, who are chasing the J-League title, and JEF United Chiba, battling to avoid relegation, rested key players in the cup competition.
Oita made ten changes to last Wednesday’s team that lost 2-0 to Sagan Tosu in the cup.
Ex-Liverpool number two Alex Miller rested seven players as the Chiba club lost 1-0 at Shimizu.
J-League rules state that all clubs should pick their strongest teams but that does not apply to the Emperor's Cup.
But JFA chief Motoaki Inukai said, "This is not really a question of rules."
"We want to make sure this kind of thing does not happen again," agreed J. League chairman Kenji Onitake.
Both clubs could be banned from next year’s competition..