Ahmadinejad has dismissed murder of six million Jews by the Nazis and their allies as a myth, saying the crime was exaggerated to bolster Israeli interests.
Haroun Yashayaei, the head of Iran's Jewish community, sent a letter of complaint to Ahmadinejad two weeks ago.
"How is it possible to ignore all of the undeniable evidence existing for the exile and massacre of the Jews in Europe during World War Two?" said a copy of Yashayaei's letter faxed to Reuters on Sunday.
"Challenging one of the most obvious and saddening events of 20th-century humanity has created astonishment among the people of the world and spread fear and anxiety among the small Jewish community of Iran," the letter added.
A Jewish community leader said he preferred not to comment on whether Ahmadinejad had sent a reply to the letter, penned on behalf on the entire Jewish community.
Jews occupy an awkward position in Israel's arch-foe Iran, often speaking out against Israeli treatment of Palestinians.
Ayatollah Ruhollah Khomeini, spiritual father of Iran's 1979 Islamic revolution, urged Iranians to distinguish clearly between their own ancient community and Zionists.
However, Iran's Jewish community has slumped to some 25,000 members from about 85,000 at the time of the revolution. Iran's population is about 69 million.
Iran's Jews are often the subject of intense suspicion and 10 from the southern city of Shiraz were convicted of spying in 2000. The closed door trial sparked international outrage.
The last five detained were released in April 2003.
Last April, Iran's Jewish parliamentarian had to complain to parliament that popular television serials were anti-Semitic. The parliament speaker supported his complaint.
Iran's Jews are sometimes called "Esther's Children". The Jewess Esther, a queen of Persia who gave her name to a book of the Bible, is buried in the Western Iranian city of Hamadan.