South Africa's anti-corruption watchdog has accused the India-born Gupta brothers of using their friendship with Zuma to influence policy and amass wealth.
Zuma and the Gupta brothers deny any wrongdoing.
Amrendra Kumar, a senior income tax official in Uttar Pradesh, told Reuters that the Gupta brothers were suspected of finding ways to bring "illicit money" they had earned abroad into India.
"We want to look into blocking that way," Mr Kumar said by telephone, adding that he was involved in ongoing raids.
"They make all kind of illegal money there outside, these are the allegations which we want to look into," he said.
The three Gupta brothers, Atul, Ajay and Rajesh, went to South Africa in the early 1990s and built a commercial empire stretching from computers to mining and media.
South Africa's chief prosecutor declared Ajay Gupta a "fugitive from justice" after he failed to report to police investigators.
On Tuesday, officials conducted raids at residences of the Guptas in the town of Saharanpur in Uttar Pradesh and the nearby town of Dehradun, as well as one of their offices in the capital, New Delhi, Mr Kumar said.
A top judge in South Africa will investigate whether the Guptas sought to influence the appointment of cabinet ministers there and were unlawfully awarded state tenders.
South Africa's new president, Cyril Ramaphosa, has made fighting corruption a top priority.