The Russian side posted a message on Twitter and captioned a video of some of their black players as "see how the chocolates melt in the sun" during a warm-weather training camp in Dubai - it was later deleted after being visible for a number of hours.
Spartak Moscow, Russian league champs past year, later posted a video in which one of the three Brazilian players in the earlier post, Fernando, denied there was any racism at the club.
Ant-racism group Kick It Out were among the first to protest about the caption beneath it - which was followed by three "chocolate bar" emojis.
The footage prompted criticism on social media and was followed up with a disapproving statement by Federation Internationale de Football Association, but the club has responded with a new video message featuring the players concerned.
Spartak had seemingly turned its Twitter account over to defender Georgy Dzhikiya for the day. "We are a friendly family". Dzhikiya was reportedly speaking the same phrase in the video.
He added: "I love you my friend".
Speaking to BBC Sport, Piara Powar, executive director of Football Against Racism in Europe, highlighted the troubling nature of the tweet in a year when Russian Federation are set to host the World Cup.
Spartak were instantly condemned on Twitter after posting the video with social media users calling the club a "disgrace" and accusing them of racism.
The tweet comes just six months before Russian Federation hosts its first ever World Cup, and one week after Liverpool officially complained to UEFA over alleged racist abuse aimed at Rhian Brewster from Spartak players in the U19 match in December.
"This shows a shocking level of ignorance. References like this show how some minorities are seen by some in the country", Piara Powar, the head of FARE, said in a statement.
They are also now being investigated by UEFA over allegations that Reds youngster Rhian Brewster was racially abused during a UEFA Youth League match at the Spartak Academy in Moscow back in December.
Spartak defender Leonid Mironov has also been charged with racially abusing Liverpool striker Rhian Brewster.