Krzysztof Charamsa said the priesthood was "full of homosexuals" and accused the Vatican of being hypocritical for banning gay clergy.
He was sacked from his senior post in Rome in early October after he revealed his sexuality at a press conference the day before a Church meeting on the family.
Now Mr Charamsa has published a letter he sent to Pope Francis on the same day.
It said the Church was "persecuting" and causing "immeasurable suffering" to gay people and their families.
The letter, sent to the BBC by the priest, also said he had to "publicly reject the violence of the Church towards homosexual, lesbian, bisexual, transsexual and intersexual people" after a "long and tormented period of discernment and prayer".
The Church is "frequently violently homophobic" he said and he called for "all gay cardinals, gay bishops and gay priests [to] have the courage to abandon this insensitive, unfair and brutal Church".
He said he can no longer cope with the "homophobic hate of the Church, the exclusion, the marginalisation and the stigmatisation of people like me" whose "human rights are denied" by the Vatican.
Mr Charamsa urged the Church to do a u-turn on a decision taken by Pope Emeritus Benedict XVI which banned gay men from becoming priests.
He said the statement that homosexuality was "a strong tendency ordered toward an intrinsic moral evil" was "diabolical".
The Catholic Church's Synod on the Family ended without any change to the way gay people were treated.
A document released after the meeting said that LGBT people should not face discrimination but added that there were "absolutely no grounds" for gay marriage.
