The southern city of Krasnodar, which boasts two clubs, FK Krasnodar and Kuban, in Russia's top flight, was overlooked last week when FIFA and the local organising committee (LOC) picked 11 cities that will host the 32-team tournament.
Saransk, the smallest of the contenders and with little soccer tradition, was considered an outsider but made the list at the expense of Krasnodar.
"We would like to express our outrage regarding the decision to exclude Krasnodar from the list of host cities for the 2018 World Cup," the Kuban fans said in an open letter addressed to Putin, Blatter as well as LOC head Vitaly Mutko and posted on their official website (greenmile.ru).
"We also express our mistrust in those officials who had been in charge of picking the host cities."
The fans, who call themselves 'greenmile' because of the club's colours, called Krasnodar "the soccer capital of Russia".
"There is no other city in Russia where the number one sport is as popular as it is here," the letter said.
"Despite the fact that Krasnodar's population is only 750,000 and our club has never won any major trophies, our 30,000-seat stadium has always been filled to capacity."
The fans added that they would not rule out any protests in the future, although they would show warm welcome to the Russian national team when it hosts the United States in next month's friendly. (Reporting By Gennady Fyodorov, editing by Pritha Sarkar)