General Srilal Weerasooriva is in South Africa as part of an international delegation attending the Association of Military Christian Fellowships - Global Interaction 2014 at the naval base of Simonstown.
The general and his wife Dilhani led a worship and evening session at the event.
In a statement, South African Tamil Federation (SATF) confirmed charges were pressed against him with the Commissioner of the Special Unit for Foreign Crimes in South Africa for alleged violation of human rights during his tenure as the Commanding Officer of the Sri Lankan Army in the 1990s.
SATF got support from another group called Solidarity Group for Peace and Justice in Sri Lanka, which has strongly condemned Weerasooriya's presence in South Africa.
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Both organisations made it clear that they acknowledged the fellowship conference as a project for the betterment of the people of South Africa, but said Weerasooriya's presence would tarnish that image.
They also demanded from the Association of Military Christian Fellowship to unreservedly apologise to South Africans for their lack of foresight in investigating the retired General and for inviting him to the country.
The Association could not be reached despite repeated calls.
According to the United Nations, 30,000 people were killed towards the end of the ethnic conflict in 2009 when the Liberation Tigers of Tamil Eelam (LTTE) was finally crushed.