Archbishop Maria Calist Soosa Pakiam of Trivandrum, the capital city of the state of Kerala, wrote a pastoral letter to his parishioners about the proposed Vizhinjam port, outlining his concerns.
In it, he said he could not approve of the port, because it will destroy 32 fishing communities home to around 50,000 people.
He said in the letter: "We are viewing this as a human rights issue. We are not against development.
"What we demand is the protection of the rights of a group that is going to suffer the most."
The Vizhinjam port has been delayed for more than two decades. Construction of the site, which would span several kilometres, is set to begin on August 17.
The government of Kerala has said it will continue discussions with the Latin-rite Trivandrum archdiocese over Vizhinjam port.
K. Babu, the state minister for fisheries and ports told Catholic news agency ucanews.com: "We will continue our discussions and remove all their fears and grievances."