The ABC understands Mr Morrison arrived in Jaffna by helicopter yesterday afternoon after attending the inauguration of two customs boats donated by Canberra to Colombo.
Mr Morrison was accompanied by the Australian High Commissioner and other Australian officials.
Jaffna was the scene of some of the worst fighting during the civil war and some Tamils there say they still face persecution.
The major Tamil political party in Jaffna says Mr Morrison met only with the governor of Northern Province in Jaffna, GA Chandrasiri, who is a presidential appointee, and not with any Tamil politicians or civil society groups.
He did not meet the chief minister of Northern Province, CV Vigneshwaran, who was elected by popular vote in last October's elections, held for the first time since 1988.
His party, the Tamil National Alliance, secured a landslide victory in the first ever elections in more than 30 years of war.
Tamil groups have accused Australia of ignoring human rights abuses in Sri Lanka in exchange for cooperation from Colombo on people smuggling and migration issues.
Meanwhile, a member of the Sri Lankan parliament has urged his government to eradicate the problems that led their citizens to seek asylum overseas.
The Australian High Court is still deciding what lawful action the Federal Government can take in regards to a boat carrying 153 Tamil Asylum Seekers that was intercepted off the coast of Australia.
Another group of asylum seekers was handed to the Sri Lankan navy on Sunday and have appeared in court in the southern city of Galle.
Sri Lankan MP doctor Rajiva Wijesingha told the ABC's Late Night Live program that factors pushing people out of the country must be diminished.
"I think it's up to the Sri Lankan government to try to reduce the causes of disaffection and indeed to develop situations in which Sri Lankans, both Sinhalese and Tamils, don't think that the best part of Sri Lanka is the sea leading out of it," he said.