"We have sought a report from our High Commission in UK about the whole issue," Secretary in the ministry, A Didar Singh told PTI.
The move followed media reports which said the Indian High Commission refused a PIO card to the eminent author as he did not have proper documents, he said.
According to the media report, Naipaul's wife Nadira, three months ago, travelled from Wiltshire to London to ask the Indian High Commission as to how her husband could apply for a PIO card.
As per Nadira, she was told by officials in the mission that her husband should travel to Gorakhpur in Uttar Pradesh to find a tehsildar or magistrate willing to certify that the eminent author is indeed a person of Indian origin, the report said.
When asked whether government was willing to waive off requirement of essential documents for the author, if he applies for the card, Singh said, "It will have to be examined what kind of documents the renowned author has. We will get to know about all this after getting the report."
Singh said any Indian origin person can get a "nativity certificate" through the mission concerned and one need not to travel to his or her place of origin for getting a certificate. A PIO card holder does not require a separate visa for India and the card is valid for 15 years.
Naipaul's wife also claimed that she was first made to wait in the "pits" of the embassy before being allowed to see an officer to whom she explained what she wanted.
However, rejecting the reports the Indian High Commission on Monday issued a statement saying Naipaul has not approached it for a PIO card
In a brief statement, the mission said, "Lady Nadira Naipaul had visited the High Commission some three months ago and made enquiries about the procedure for application for a PIO card for her husband which were explained to her by the concerned officials of the mission."
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