The news comes a day after McCain rejected the endorsement of another pastor, John Hagee, who has said he believes the Nazis performed God's will by carrying out the Holocaust in order for Israel to be established.
The Huffington Post website reported on Thursday that Hagee, a well-known television evangelist who oversees a church in San Antonio, Texas, gave a sermon in the late 1990s in which he quoted from the Bible to make the argument that God had influenced Nazism.
Hagee is a strong supporter of Israel and is the founder and national chairman of the Christians United for Israel group.
However, on Friday he said that his work had been "mischaracterised and attacked", and rejected any charges of anti-Semitism.
He said that he "in no way condones the Holocaust or "that monster Adolf Hitler".
McCain in turn said he wished to emphasise that Hagee had never been his pastor.
"I did not know of them before Reverend Hagee's endorsement, and I feel I must reject his endorsement as well," McCain said.
Hagee had previously referred to the Roman Catholic Church as "the great whore" and called it a "false cult system".
He also has linked Hitler to the Catholic Church, suggesting it helped shape his anti-Semitism.
Hagee also said Hurricane Katrina was God's retribution for homosexuality.
McCain's pastor problems have been linked to that surrounding Jeremiah Wright, a former pastor of Barack Obama, the US Democratic presidential hopeful and Illinois senator.
Wright resigned from Obama's campaign after sermons surfaced on the internet in which he blamed the US government for the September 11, 2001, attacks.
Obama distanced himself from Wright after the pastor stood by his comments about those attacks being the result "America's chickens ... coming home to roost".
Wright had presided over Obama's marriage and baptised his two daughters.