Parrikar met the Archbishop before tendering his resignation to Goa Governor Mridula Sinha.
"There is a mix reaction over you taking over as a union minister," the Archbishop told Parrikar during an informal meeting.
Parrikar also paid visit to three local temples.
"There was lot of pressure on me not to leave the state. But I had to take it in the interest of nation," Parrikar, told Archbishop Ferrao.
The BJP legislative wing had six catholic MLAs which is unprecedented for the party, earlier labelled as communal.