Only a small, politically-motivated group was responsible for the harassment of Sri Lankan visitors and they were receiving no encouragement whatsoever from the central Indian government, he said in his first public reaction on the issue.
He said the Indian government has responded positively to Sri Lanka's request to guarantee the safety of its citizens.
"We would only deal with the centre and would not deal with state governments", Rajapaksa told reporters here.
Sri Lankan government facilitated the return of some 184 of its nationals on a pilgrimage to a church in Tamil Nadu, early this week. The bus they were travelling in had come under attack in Thanjavur.
Sri Lanka responded by issuing a travel advisory against travel to Tamil Nadu.
The pilgrims, mostly from the north-western town of Chilaw, upon return said a few of them sustained injuries from the attack.
Rajapaksa said he would discuss with Indian authorities the safety of Sri Lankans if the opportunity was made available to him during his visit to India commencing on September 19.
He is due to visit Sanchi in Madhya Pradesh to lay the foundation stone for a centre for Buddhist studies.
He is also expected to have an audience with Prime Minister Manmohan Singh.
Rajapaksa's comments came as an ultra-nationalist Sinhala group, Patriotic National Movement, urged him to refrain from visiting India.
"What sense does it make when president visits India when his government had warned the citizens of the country not to travel there?" asked its chief Gunadasa Amarasekera.
