Demonstrators led by women held photographs of their missing relatives outside the Jaffna library and urged Pillay, the United Nations High Commissioner for Human Rights, to intervene.
"There were women whose sons, brothers and husbands had disappeared in recent years," a resident told AFP by phone, asking not to be named. "Some of them were weeping. They could not meet with the UN visitor.
"
A government census report released in February last year showed 6,350 people were reported missing in the north after fighting ended in 2009, while rights groups say "disappearances" are still a problem.
The demonstration in Jaffna, 400 kilometres (250 miles) north of Colombo, was in contrast a protest in the capital Monday.
Pro-government Buddhist monks in Colombo had denounced Pillay, who had called for a war crimes investigation in Sri Lanka.
Pillay, who has previously been accused by Colombo of overstepping her mandate, arrived Sunday for her first official visit after the government dr