"Travel to all other states in India are safe for Sri Lanka nationals."
The foreign ministry said Sri Lanka "regrets the increasing number of instances of intimidation of Sri Lankan nationals visiting Tamil Nadu for the purposes of tourism, religious pilgrimages, sporting and cultural activities and professional training."
"These visits are a reflection of people to people contact between the polity of two countries which are bound by age old friendly ties and traditions," the foreign ministry said.
"Most recently today, 184 pilgrims visiting the Poornimatha Church in Thanjavur have been mobbed and become refuge in the church. The Government of Sri Lanka has taken all steps required through the Indian Government to seek the safety of these pilgrims."
The incident with Catholic pilgrims is the latest in a series of incidents that have raised tensions between Sri Lanka and Tamil Nadu state.
Earlier this week Tamil Nadu chief minister J Jayalalithaa ordered a Sri Lankan football team to be sent back and suspended a state official for allowing them to play a friendly match in Chennai.Jayalalithaa has objected to members of Sri Lanka's military being trained in India.
Uneasy relations between Sri Lanka and the South Indian state has soured further the end of a 30-year war with Tamil Tiger separatists in 2009, with political groups in the state revving up calls for war crimes probes against Sri Lanka's military and fishing dispute also flaring up.