The 73 year-old began suffering pain earlier this year similar to 1998, when he was diagnosed with prostate cancer and underwent surgery. He said doctors discovered an ulcer in his anal area during a visit to Cuba in March.
Since then, he has dropped more than nine kilograms while battling serious infection and inflammation.
Mr Farrakhan said he will work hard to recover "because I do not believe my earthly work is done." He has asked his executive board to solve problems during his recovery.
Farrakhan likened his situation to that of Fidel Castro, who temporarily relinquished power because of illness.
"While many rejoiced -- believing and thinking that if Fidel
Castro and the Cuban Revolution expired they could move Cuba and the Revolution in a new direction -- his absence from the helm only proved that Cuba will not fall apart over the absence or passing of their illustrious leader," Farrakhan wrote in the letter.
He also warned followers to be "ever watchful for any smart, crooked deceiver and hypocrite who would create confusion over my present condition."
Group’s future in doubt
Experts say Farrakhan's death could seriously alter the future of the Nation of Islam.
"Through the organisation's history, the death of a leader has meant a number of divisions," said Lawrence Mamiya, a professor of religion and Africana studies at Vassar College in Poughkeepsie, New York.
After the death of Nation leader Elijah Muhammad in 1975, the organisation split. Since then there have been several smaller divisions.