Ahir's criticism came after Varun expressed his views in an article in a Hindi daily.
Following the MoS Home Affair's remarks, Varun tweeted today that his article focused primarily on defining India's asylum policy, with clear demarcations on how "we would accept refugees".
"As for the Rohingyas, I've called for empathy, leading potentially to asylum, while vetting each applicant for national security concerns (sic)," he tweeted.
Varun's remarks were at variance with the government's stand on the issue.
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Terming the Rohingya refugees as "illegal" immigrants, the government had recently told the Supreme Court that some of them were part of a "sinister" design of Pakistan's ISI and terror groups such as the ISIS, whose presence in the country will pose a "serious" national security threat.
Home Minister Rajnath Singh had also last week said Rohingyas were not refugees who have applied for asylum in India but illegal immigrants who "will be deported".