On Monday Sri Lanka issued a travel advisory asking citizens not to travel to Tamil Nadu after an attack on pilgrims visiting a church.
On Tuesday 178 Sri Lankan visitors to a Christian shrine in Velankanni were stopped by protestors, and in another instance five buses of pilgrims stoned, Indian reports said.
Sri Lanka's foreign ministry said 184 pilgrims who had earlier taken refuge at Poornimatha Church in Thanjavur had been taken in buses to Trichy airport assisted by Indian authorities and staff of deputy high commission (embassy) in Chennai
"It was also reported that the buses had come under attack en route to the airport by a group of protesters," Sri Lanka's foreign ministry said.
"However, the Government of India has provided the pilgrims security and safe passage, and taken them to a tourist lodge, near the airport until their departure.
"A special flight has been arranged by the Government of Sri Lanka for the group of pilgrims to return to Colombo tonight from Trichy.