The capital club's old coach claims that the controversial AC Milan striker was jeered because of his poor attitude on and off the pitch as opposed to the colour of his skin
Play was stopped during the second half of the 0-0 match between the Serie A sides, with referee Gianluca Rocchi having to ask Giallorossi captain Francesco Totti to plead with the offending ultras personally before play could continue.
Roma were subsequently fined €50,000 (£42,200) for the chants but Zeman has is adamant that his attitude on the pitch led to the jeers.
"They did not whistle Balotelli because of his skin colour but his attitude," he told RTL 102.5. "He can be controversial at times.
"The problem is not the colour of the skin but the behaviour. If a player performs well, nothing happens."
Roma's final match of the Serie A season sees them face Napoli on May 19 before they take on Lazio in the Coppa Italia final.