Barcelona manager Ernesto Valverde said “Messi finishing 5th in this year’s Ballon D’Or is absurd”.
Real Madrid midfielder Luka Modric won the prize, awarded by France Football and voted for by 180 journalists.
Barcelona and Argentina forward Messi, 31, finished outside the top three for the first time since 2006, having won the award five times.
“We congratulate Modric for winning the Ballon d’Or but Messi being in fifth place is absurd,” said Valverde.
“I will not get into discussing the inconsistencies of the prize.”
Messi won a record fifth Golden Shoe for finishing as Europe’s leading scorer last season, with 34 goals as Barcelona won La Liga and the Copa del Rey.
Messi’s 280 points in the voting left him behind Modric (753), Juventus forward Cristiano Ronaldo (476), Atletico Madrid striker Antoine Griezmann (414) and Paris St-Germain forward Kylian Mbappe (347).