Rijiju, who handles the visa issue in the home ministry, said Isa should have applied for conference visa rather than applying for tourist visa.
China accuses Isa of terror activities in the remote Xinjiang region where there is frequent violence between the local Uyghur population and government forces.
The Trump administration has revoked Harvard University's eligibility to enrol foreign students, raising concerns over the legal status of thousands of students, including nearly 800 from India, currently enrolled at the varsity.
"India has made a cogitative decision, and shows the common views of China and India in fighting terrorism and separatism, and the determination of further cooperation," Fu Xiaoqiang, an expert on South Asian studies at the China Institutes of Contemporary International Relations, told the Global Times.
It is not a protest but China's concerns have been conveyed to India, they said.
Waltz after being elected as the Co-Chair of India Caucus in January last year had said that India is the world's largest democracy and an important strategic partner for the United States.
Isa had "suppressed" facts while obtaining it but admitted that China had made its position clear to New Delhi.
Ministry of home affairs confirmed that Isa's visa has been withdrawn immigration sources added that the decision was not taken under Chinese pressure.
Before the 2014 Lok Sabha elections, Modi had criticised Manmohan Singh's policy towards China and promised a more strong-willed policy. Those claims are now under a cloud.
In Tokyo, hundreds of Japanese citizens came out on the streets to express solidarity with the oppressed people of Tibet, Xinjiang, Mongolia, Hong Kong and Taiwan.
Significantly, reveals Rajeev Sharma, the MEA was not even consulted on the Dolkun Isa issue.
Released by secretary of state Antony Blinken, the annual human rights reports of the state department is a mandatory requirement of the US Congress giving details of human rights status in countries across the world.
'Unless India ups the ante, Beijing will continue to believe its transgressions are cost free and will feel encouraged to do more of the same.'
Why is China's supreme leader promoting Han Chauvinism so aggressively, asks Claude Arpi.
There is growing alarm at the inexorable rise of China, both of its military prowess and its aggressive bullying of other countries plus its subjugation of whole portions of its own population.
Nancy Pelosi's gritty refusal to backtrack on her plans to visit Taiwan is part of who she is.
The battle against militants fighting for separation of China's volatile Xinjiang province, bordering PoK and Afghanistan, is getting "tougher, fiercer and crueler than ever" due to the revival of pan-Islamic extremist groups, top Chinese leaders from the province said.
The first priority for the new Tibetan administration in Dharamsala should be to look at Tibetan recruitment in the PLA, suggests Claude Arpi.
'Why did your generals try to grab a few square kilometres of Indian territory in Ladakh?' 'And what happened to the hard work that you and Prime Minister Modi put into the Wuhan and Mamallapuram meets?' Claude Arpi writes a letter to Xi Jinping, China's self-styled supreme leader, who turns 68 today, June 15.
'He still has to deal with party norms and traditions and has been careful to follow the order of seniority,' points out Claude Arpi.