The two countries agreed to share more intelligence at the start of an overnight visit to Sri Lanka by Thai Prime Minister Yingluck Shinawatra, the presidential secretariat said in a statement.
"We must cooperate more closely in security-related information and intelligence sharing," the statement quoted Rajapakse as saying during bilateral talks in Colombo.
It said the two leaders "agreed to enhance cooperation in defence and maritime security", but gave no further details.
However, it said Rajapakse "pointed out" that despite his troops crushing Tamil Tiger guerrillas in a major offensive in 2009, supporters of the defeated rebels were continuing their separatist campaign from overseas.
Sri Lanka faces international censure over its no-holds-barred military campaign, but denies allegations that up to 40,000 civilians perished in the final offensive that ended in May 2009.
There have been no attacks blamed on the Tamil Tigers in Sri Lanka since the middle of that year.
Mea