The system will be coordinated by world football's ruling body and implemented in cooperation with the European anti-discrimination organisation FARE.
Any incidents of discrimination or racism will be reported to FIFA which has pledged to impose disciplinary sanctions on any countries involved.
The implementation of the new system is particularly apt as racism is rife in football in Russia, hosts of the 2018 World Cup.
More than 200 acts of racism were committed by Russian fans between 2012 and 2014 according to a recent report by the Sova Center, a Moscow-based racism-monitoring group.
Last month FIFA president Sepp Blatter said "a lot of work needs to be done" to wipe the scourge of racism and discrimination from Russian football and the game in general.
FIFA and European football's governing body UEFA have often handed out relatively minor punishments when incidents have occurred in the past.
Manchester City midfielder Yaya Toure said there needed to be tougher action against racist behaviour.
"For me the real matter is we need to take real sanctions," he said at the launch of the FIFA initiative.
"We can see we have a couple of clubs that are bigger than a country now and pay maybe 20 thousand and something like that for me is not enough. We need to do more."
(Reporting by Mike Collett, editing by Tony Jimenez)
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