Swiss Blatter also pointed out in a statement issued by football's governing body that Chung was an influential member of FIFA for 17 years until 2011.
The 63-year-old billionaire scion of Korea's Hyundai industrial conglomerate launched his bid for the presidency in Paris earlier on Monday with a stinging attack on Blatter and Michel Platini, head of European football's ruling body UEFA.
Platini is another candidate to replace Blatter at the election on Feb. 26.
"It is disturbing, to say the least, to hear Dr Chung Mong-joon describe FIFA as a 'corrupt organisation' during a press conference announcing his candidacy," said Blatter.
"Even more so when one recalls, and as Dr Chung cannot have forgotten, that he was a FIFA vice-president and a FIFA emergency committee member for 17 years from 1994 until 2011.
"Regarding personal attacks made by Dr Chung at the same event, I will not comment further than to say that this is particularly disrespectful to all concerned.
"I would like to stress again that FIFA is dedicated to improving the organisation and will continue to strengthen its governance and accountability," added Blatter.
"Our work in this area continuously evolves and we are focussed on achieving the highest standards for the international football community."
During his speech and press conference, Chung made several references to corruption at FIFA.
"Michel Platini was a great football player and he is my friend," said the Korean. "His problem is he does not seem to appreciate the seriousness of the corruption crisis at FIFA.
Chung also said "the problem at FIFA is that those mired in corruption, the only thing they are interested in is hiding the corruption".
He added that the core issue for the election "is whether the 40-year-old system of corruption should continue or not".
In a reference to Blatter, Chung added: "The real reason FIFA has become such a corrupt organisation is because the same person and his cronies have been running it for 40 years".
Blatter was secretary general for 17 years before being elected president in 1998.
(Editing by Tony Jimenez)
