China accuses Isa of terror activities in the remote Xinjiang region where there is frequent violence between the local Uyghur population and government forces.
Rijiju, who handles the visa issue in the home ministry, said Isa should have applied for conference visa rather than applying for tourist visa.
Isa had "suppressed" facts while obtaining it but admitted that China had made its position clear to New Delhi.
"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.
Ministry of home affairs confirmed that Isa's visa has been withdrawn immigration sources added that the decision was not taken under Chinese pressure.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.
Significantly, reveals Rajeev Sharma, the MEA was not even consulted on the Dolkun Isa issue.
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