The decision relates to the conduct of supporters of both nations during their opening round matches, in which certain fans are believed to have directed racist chants at opposition players.
A statement on its official website read: “Uefa has opened disciplinary proceedings against the Royal Spanish Football Federation (RFEF) for the improper conduct of their supporters (racist behaviour, racist chanting) at the Uefa EURO 2012 Group C match against Italy in Gdansk on Sunday 10 June.
“Disciplinary proceedings have also been opened against the Russian Football Union (RFS) for the improper conduct of their supporters (racist behaviour, racist chanting) at the Uefa EURO 2012 Group A match against the Czech Republic in Wroclaw on Friday 8 June.
“The Uefa Control and Disciplinary Body will deal with these cases on Thursday 28 June.”
Spanish supporters were heard directing racist chants at Italy striker Mario Balotelli in their 1-1 draw two weeks ago, whilst Czech Republic defender Theodor Gebre Selassie told reporters he had 'noticed' similar behaviour from Russian fans during the opening match of Group A.
The news is the latest in a string of racist issues to have blighted the tournament in Poland and Ukraine so far.
The Croatian FA was fined €80,000 after a section of supporters directed abuse at Balotelli during their 1-1 draw with Italy in the group stages.
Players from the Netherlands also complained after a minority of fans could be heard aiming monkey noises at them during an open training session.
A number of players had raised concerns before the start of the tournament that racist chanting could become a feature of the tournament this summer, although Uefa insisted it would come down hard on any such cases.
Russia has already been in hot water with European football's governing body after violence erupted between supporters after the match with Czech Republic and in the build-up to their clash with co-hosts Poland.
Spain, meanwhile, have received a reprimand for racist chanting in the past. In 2004, the Spanish FA was fined more than €50,000 after several England players suffered abuse from fans in Madrid during a friendly match.