Messi's Barcelona team-mate Neymar comes out on top of the list compiled by the Swiss-based study centre, which estimates the value of the 110 most desirable players in Europe's top five leagues, using an algorithm based on analysis of almost 2,000 paying fee transfers.
Neymar is valued at €210.7million (A$311 million) under criteria considering performance, club, international status, age, position and marketability.
However, Messi, who turns 30 later this month and is reportedly on the verge of extending his contract at Camp Nou, comes in fourth on €151.7 (A$224 million), with England internationals Alli and Kane pipping him on €155.1m (A$233 million) and €153.6m (A$227 million) respectively following superb seasons for Spurs.
Ronaldo is favourite to match Messi with a fifth Ballon d'Or at the end of the year, having inspired Real Madrid to LaLiga and Champions League glory.
However, the 32-year-old comes in at €112.4m (A$166 million) in the CIES standings, below Antoine Griezmann, Luis Suarez, Paul Pogba, Gonzalo Higuain, Eden Hazard and Paulo Dybala.
Ronaldo is the oldest player on the list, with Monaco sensation Kylian Mbappe the youngest.
Despite being linked with a world record move to Real Madrid, Mbappe only registers €92.6 million (A$136 million) , ranking him below the likes of Manchester City's Raheem Sterling and Atletico Madrid's Yannick Carrasco.
Manchester United's often-derided move to make Pogba the most expensive player in the world represents value for money in the CIES figures, although the previous holder of that accolade – Real Madrid's Gareth Bale – finds himself down in 43rd position on €66.7 million (A$99 million) after an injury ravaged campaign.
CIES Football Observatory transfer value estimates – top 25
Neymar – Barcelona €210.7m
Dele Alli – Tottenham €155.1m
Harry Kane – Tottenham €153.6m
Lionel Messi – Barcelona €151.7m
Antoine Griezmann - Atletico Madrid €150.3m
Luis Suarez – Barcelona €140.8m
Paul Pogba - Manchester United €134.3m
Gonzalo Higuain – Juventus €120.2m
Eden Hazard – Chelsea €117.2m
Paulo Dybala – Juventus €115.3m
Cristiano Ronaldo - Real Madrid €112.4m
Kevin de Bruyne - Manchester City €110.5m
Romelu Lukaku – Everton €105.4m
Robert Lewandowski - Bayern Munich €100.6m
Raheem Sterling - Manchester City €98.8m
Yannick Carrasco - Atletico Madrid €97.6m
Alexis Sanchez – Arsenal €95.9m
Kylian Mbappe – Monaco €92.6m
Ousmane Dembele - Borussia Dortmund €87.1m
Roberto Firmino – Liverpool €85.3
Eric Dier – Tottenham €85m
Diego Costa – Chelsea €83.4m
Edinson Cavani – PSG €82.8m
Christian Eriksen – Tottenham €82.5m