"It has unfortunately been noted that some people write words and sentences on banknotes or stamp them with emblems," the bank said in a statement carried by the official IRNA news agency.
"Those who have such banknotes should exchange them in banks across Iran and people must avoid writing on banknotes," it said, adding that the bank replaced about 700 million a year.
It did not elaborate on what was being written but since mass protests broke out against hardline President Mahmoud Ahmadinejad's disputed June re-election, anti-government slogans such as "Death to the Dictator" have appeared on banknotes.
Opponents of the president have also sprayed graffiti on walls around Tehran, using the signature green of the opposition which was also the chosen campaign colour of Ahmadinejad's main challenger in the election, former prime minister Mir Hossein Mousavi.
Many transactions are carried out in cash in Iran, which is under US and UN banking sanctions and where international credit cards cannot be used.
Higher denomination banknotes all carry a picture of revolutionary leader Ayatollah Ruhollah Khomeini.
New protests erupted in Iran this week after the death of top dissident cleric and opposition supporter Grand Ayatollah Hossein Ali Montazeri. Mourners clashed with security forces in central Iran on Wednesday and dozens were arrested.
Authorities has also vowed to crack down on any protests during the Shiite festival of Ashura which reaches its climax on Sunday.
