The Cameroonian striker, who has been singled out for racial abuse during his career, said he had been shocked by video footage last month showing a group of Chelsea fans preventing a black man boarding a metro train in Paris.
"I was shocked when I saw those images, but fortunately Chelsea has millions of fans worldwide," African football's most decorated player told Reuters before the presentation at Kensington Palace.
"These five or 10 fans are not representative of all the other fans," added the four times African player of the year and twice African Nations Cup winner.
"We are here to fight against these issues and try to have harsher laws that are applied in a very tough way to fight against this abuse."
Eto'o, now playing for Sampdoria in Italy, was awarded the European Medal of Tolerance by the European Council on Tolerance and Reconciliation (ECTR), a non-governmental campaigning organisation.
"Football is a very important vehicle to fight racism, Islamic radicalism, neo-nazism and anti-semitism," said ECTR president Moshe Kantor, who warned of a growing problem in Europe.
The Russian-born Kantor, who is also president of the European Jewish Congress, praised Eto'o for having the "courage and will to stand against the racists, building awareness and inspiring fellow footballers and millions of football fans."
Eto'o has played for Real Madrid, Barcelona, Inter Milan, Anzhi Makhachkala and Everton in a career that has seen him win the Champions League three times.
He experienced racism in Spain in 2006, while with Barcelona, when he threatened to walk off after Zaragoza supporters made monkey noises whenever he had the ball.
In Italy, playing for Inter against Cagliari, the referee stopped the match when Cagliari fans made racist chants. Eto'o went on to score the winning goal.
Eto'o played down the risk of racism tarnishing the 2018 World Cup in Russia, however, despite numerous examples plaguing the country's domestic game and causing concern abroad.
"My experience in Russia was the most beautiful of my sporting career," he said. "I came away with a very good impression."
(Reporting by Alan Baldwin, editing by Justin Palmer)
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