Vandals broke through the gate of St Alphonsa's Church in Vasunt Kunj area of Delhi in the early hours of Monday night.
The group scatted communion over the floor of a room inside the church and stole a chalice.
Since December Christians in the area have seen a number of attacks including a Church being set alight and a nativity scene destroyed.
Church leaders are calling on the Indian government to offer more protection to Christians.
In January a group of Catholic bishops met with Prime Minister Narendara Modi to ask for his help in stopping Christian persecution.