Pillai, on a week long assessment visit of the country, was having meetings in the Jaffna library when the kith and kin of the disappeared demonstrated outside, demanding her intervention to trace them.
Women, mostly Tamil, held placards showing portraits of their disappeared kin.
Among them was the wife of Prageeth Eknaligoda, a Sinhala cartoonist whose whereabouts has not been know since 2010.
Military defeated the LTTE in May 2009, putting an end to their bid to create a separate state for Tamils.
More From This Section
According to human rights groups, over 500 people had disappeared from Jaffna during the military's victorious onslaught against the LTTE.
According to a UN report, Sri Lankan army might have killed 40,000 Tamil civilians in the final phase of the war.
Sri Lanka has come under intense international pressure to probe disappearances and rights abuses allegedly happened during the military campaign.