The Rev. Fred Luter said Hurricane Katrina in 2005 profoundly affected Nagin, a Democrat who served from 2001-2010.
"He is a good and decent man who made some unwise choices and decisions during a very difficult and traumatic time in his personal and professional life,'' Luter wrote in one of numerous letters made public Friday.
Nagin, 58, was convicted in February on 20 criminal counts including bribery, fraud and money laundering. Prosecutors said the crimes occurred before and after Katrina struck.
Some of the charges carry possible 20-year sentences. Prosecutors have not made their sentencing recommendations public, but a defense motion filed recently indicates prosecutors have recommended a sentence of 20 years.
Nagin family members and some former members of his staff also wrote on his behalf.
The letters were made public by U.S. District Judge Helen Berrigan, who allowed them to be reviewed in her chambers.
Luter, a New Orleans minister, was elected as the first African-American president of the 15.7 million-member Southern Baptist Convention in 2012.
He said Katrina affected Nagin "spiritually, emotionally, and mentally'' when it hit in 2005.
The storm caused catastrophic flooding and led to Nagin's emotional and sometimes profane plea for faster federal help.