Uyghur leader Dolkun Isa has voiced disappointment at the cancellation.
The union home ministry cancelled the tourist visa as is not a valid travel document to attend a conference, sources said.
"We have cancelled the visa given to Dolkun Isa," a home ministry spokesperson confirmed on Monday.
The World Uyghur Congress (WUC) is scheduled from April 28 to May 1 in Dharamsala, Himachal Pradesh.
It is being organised by the US-based Initiatives for China.
Voicing his disappointment at cancellation, Isa said that Indian authorities had granted him a tourist e-visa, "but it was cancelled after my visit was widely reported in the Indian press".
He said the Indian authorities cancelled the tourist visa on April 23.
"I recognize and understand the difficult position that the Indian government found itself, and regret that my trip has generated such unwarranted controversy," he said.
The conference was to see ethnic and religious communities in China as well as scholars and activists meet and openly to discuss and "exchange ideas, promote peaceful dialogue, and reinforce bonds between disparate communities".
Isa also said that China has "regularly attempted to block or interfere with my human rights work at the UN in Geneva, in particular".
The invite to the dissident Uyghur activist was bound to have rankled China.
Last week, External Affairs Minister Sushma Swaraj met with her Chinese counterpart Wang Li in Moscow on the sidelines of the Russia, India, China trilateral, while National Security Advisor Ajit Doval was in Beijing to meet with State Councillor Yang Jiechi, special representative on the Chinese side for the 19th Special Representatives' Meeting on the China-India Boundary Question.
India has raised with China its disappointment over Beijing blocking the move in the UN to ban Jaish-e-Mohamed chief Masood Azhar, the mastermind of the Pathankot attack.
China, a close friend of Pakistan, had said there were not enough grounds to ban Azhar.
The move to give Isa a visa to attend the Uyghur conference was seen as a tit-for-tat move by India. (IANS)