Father Dias met Biden during a 30-minute holy communion service for the US president at a hotel where he was staying in New Delhi on Saturday, ahead of the G20 summit.
Archbishop Anil Couto's instructions, though politically charged, are not unusual or unprecedented.
Delhi high court on Wednesday sought response of the Centre on a PIL seeking protection of religious rights of Christians and an SIT probe into the recent attacks on churches in the national capital.
Meanwhile, the Archbishops secretary, Father Robinson Rodrigues said that such prayer campaigns took place before every general election.
Scores of members of the Christian community and social activists staged a protest outside the Delhi Police headquarters in New Delhi on Tuesday morning over alleged the police inaction in the case of the fire which on Monday gutted a church in northeast Delhi's Tahirpur area.
A substantial part of a catholic church in northeast Delhi's Tahirpur area was gutted when a fire broke out at its premises on Monday morning with the Christian community suspecting foul play in the incident.