Russia's defending champions Spartak Moscow received a partial stadium ban Wednesday for monkey chants directed at Cape Verdean midfielder Nuno Rocha but a top official said the World Cup hosts are being unfairly singled out.
The football federation also fined Zenit Saint Petersburg $1,600 (1,300 euros) for "Nazi slogans" heard during a league match with the north Caucasus side Anzhi.
The twin penalties deliver a new blow to Russian football international reputation less then two months before the vast country hosts its first World Cup.
Fears of racism and hooliganism marring one of sport's most celebrated competitions have been a constant refrain throughout Russia's preparations.
The world governing body FIFA is already investigating ape noises heard during a warmup friendly against France in Saint Petersburg last month.
But Russian football's anti-racism inspector Alexei Smertin said Wednesday that his country was being unfairly singled out.
"I cannot say that (racist incidents) happen more often in Russia than in other countries," he told the RIA Novosti state news agency.
Smertin argued that Moscow's current diplomatic standoff with the West was feeding into existing biases about Russia.
"We cannot fail to take the political situation into account," said Smertin.
"There is certain bias (again Russia) in this respect."
Spartak will play their next league cup match -- not scheduled until the 2918/19 season -- with one of their stands reserved for the fans empty.
Last Wednesday's semi-final in Moscow culminated with a penalty shootout between Spartak and the small Russian Premier League side Tosno.
Rocha scored the winning spot-kick for Tosno before running past Spartak supporters while celebrating the upset.
Footage of the episode showed the 26-year-old cupping his hand to his ear as a chorus of ape noises rang down from the crowd.
The chanting appeared to begin while he was preparing to take the kick.
The Zenit incident occurred during an April 14 match against the Makhachkala side Anzhi in Saint Petersburg.
"Zenit supporters chanted Seige, Seige," said disciplinary committee chief Artur Grigoryants.
"This is classified as a Nazi slogan."
The phrase is a variant of the highly the offensive salute that was used to address Hitler.
Racial animosity between big Russian teams and smaller sides from the north Caucasus have run high in the Premier League for years.
Various forms of abuse have been plaguing Russian football since clubs began purchasing foreign players after the Soviet Union's collapse in 1991.
The Football Against Racism in Europe (FARE) anti-discrimination network reported 89 racist and far-right incidents at Russian games in the 2016/17 season.
The number was about the same as that recorded in the preceding three seasons -- a sign that Russia's campaign to clean up its game has not had the desired effect.
The World Cup final will be played on July 15 in Moscow while Saint Petersburg will host one of the semi-finals.
Both cities are home to large groups of hardcore nationalist supporters and have witnessed numerous ugly episodes during games.