The US government has said the litigation would cause "significant tension between the United States and South Africa".
Citi is considering its legal alternatives in the case, said Donna Oosthuyse, the global banking giant's chief operating officer in South Africa.
She said the company had contributed more than R25m since 1999 in programmes focused on education, literacy and community development for historically disadvantaged South Africans.
She said the projects were not reparations, but part of a business model that Citi practices everywhere.