Singh today met Rajapaksa on the sidelines of the 3rd BIMSTEC Summit here.
The Prime Minister raised the issue of Indian fishermen caught by Sri Lankan navy for allegedly violating their territorial waters.
"The prime minister said it (the fishermen issue) was a livelihood issue and must be handled in a humane manner by Sri Lanka," Indian foreign office spokesperson Syed Akbaruddin said at a briefing after the 25-minute meeting.
Their eight trawlers were seized, a Sri Lankan Naval spokesman said.
The fishermen were being taken to the port of Kankesanturai to be handed over to the fisheries surveillance officials, he said.
The frequent arrest of Indian fishermen by Sri Lankan Navy has become a major irritant in bilateral ties.