Archbishop Moses Costa of Chittagong told Catholic charity Aid to the Church in Need (ACN) that authorities were exploiting Christians and other minorities working in dangerous conditions dismantling old ships.
Stating that men have been killed in Chittagong's shipbreaking yards on the coast of southern Bangladesh, he said: "This work is carried out in very hazardous conditions and claims innumerable human lives."
But according to Bishop Costa, officials are preventing him from helping the workers.
He said: "But I am not permitted to visit this place, because the authorities have refused me permission."
Highlighting the Church's concern about the increase in violence against parishioners, he described the situation in his archdiocese as "difficult and dangerous".
With Catholics only numbering 270,000 or 0.2 percent of the country's 156 million population he described how they were often scapegoats.
Bishop Costa said: "Last year a thousand Bengalis attacked a parish in Chittagong, because many miles away two business men had been killed and we Christians were accused of having had something to do with it."
The archbishop criticised the state for not fulfilling its constitutional obligation to ensure "equal status and equal right in the practice of the Hindu, Buddhist, Christian and other religions".
He said: "The government does not acknowledge their rightful existence and ignores them, so that they have scarcely any possibility of development."
ACN is helping local Church leaders to stand up for people's rights by providing support at the Inter-Religious Dialogue Centre in Khulna.
The charity is also assisting in the spiritual development of young people in Dhaka Diocese.