The 10-metre marble statue in Yeltsin’s home town of Yekaterinburg had been unveiled last February to mark his 80th birthday.
The inscription of the late leader’s name was disfigured and blue paint daubed on it. The damage was discovered early Friday.
Yeltsin played a key role in burying the Soviet Union and became Russia’s first president. He died of heart failure in 2007.
The suspected vandals face detention of up to three months, if convicted.
The Communist Party, however, said it would pay the cost of lawyers for the offenders if they were found.
“This support is due to the fact that we share the feelings of the political vandals and fear that their right for a fair trial could be violated,” top party official Alexander Ivachyov wrote on his LiveJournal blog.