Rajapakse said he was also keen to boost bilateral trade with India, currently running at an annual two billion dollars, and explore the possibility of buying electricity.
Rajapakse, who begins a five-day "working visit" to India Saturday, said he was keen to have greater cooperation to tackle illegal traffic across the Palk Straits, the narrow strip of sea dividing the two nations.
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"Increased patrolling will also help ensure the safety of fishermen of both countries," the president said adding that Tamil Tiger rebels were targeting Indian fishermen to hijack their trawlers for smuggling in supplies.
Fishermen from both countries have repeatedly charged that they are attacked by security forces or Tamil Tiger rebels in the rich fishing grounds between the two countries.
Security forces have denied attacking fishermen, but have accused the Tigers of taking the cover of fishermen to launch attacks against the navy.