Additional Chief Metropolitan Magistrate S K Gadhvi ordered a court inquiry into the matter under CrPC section 302 on Jay Shah's complaint.
In his application, Jay prayed for, "criminal action against the respondents for defaming and tarnishing the reputation of the complainant through an article, which is scandalous, frivolous, misleading, derogatory, libelous and consisting of several defamatory statements."
In its article, the news website had claimed Jay's firm Temple Enterprise's turnover zoomed by around 16,000 times from Rs 50,000 to around Rs 80 crore in 2015-16 after the BJP came to power in 2014.
Latching on to the article, the Congress questioned Prime Minister Narendra Modi's "silence" on the issue, demanded Shah's ouster and institution of an inquiry by two judges of the Supreme Court.
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Union minister Piyush Goyal said in New Delhi that Additional Solicitor General Tushar Mehta will represent Jay Shah in the case. He said Mehta had sought Law Minister Ravi Shankar Prasad's permission to appear for Jay and the approval was granted.
"We believe that he (Jay) has been wronged and he must get justice. There is no harm if the best of lawyers appear for him. An ASG can appear in a matter between two private parties after taking permission," he told reporters.
"Did you act as a watchman (chowkidar) or were you complicit? Please say something," Gandhi tweeted in Hindi.
While tagging a copy of the news report, Gandhi had yesterday taken a jibe at the BJP chief,"We finally found the only beneficiary of Demonetisation. It's not the RBI, the poor or the farmers. It's the Shah-in-Shah of Demo. Jai Amit."
Goyal also rejected any comparison between business transactions of Amit Shah's son and those of Congress president Sonia Gandhi's son-in-law Robert Vadra. He claimed Vadra's was a case of "round-tripping of money" with help from the government while Jay had no dealing with government.
"Jay has had no dealing with government. His every transaction is official and he did his work honestly," Goyal said.
"Our conscience is clear. That is why we announced on the very day (of story's publication) that we are going to court," he said.
The Congress fielded its senior spokesman Anand Sharma in the national capital where he demanded constitution of a Commission of Inquiry with two Supreme Court judges to probe the matter.
"We demand the prime minister...he speaks a lot everyday and on each issue. He should break his silence on this issue and declare a Commission of Inquiry comprising two Supreme Court judges. There should be a neutral probe," he told reporters.
"It is a tough call for Modi. The country is looking at him whether he will choose friendship and party politics or truth and morality," Congress communications incharge Randeep Surjewala said in Jaipur.
Calling for transparency and accountability, he said, "Why shy away from probe if there is nothing wrong? There is no smoke without fire. The country was waiting for development ... but 'Jay ka Vikas ho gaya'."
In Kolkata, party spokesperson Gaurav Gogoi said Modi should prove that he is above party politics and demanded a probe into the claims made in the report.
In Coimbatore, Union minister Ananth Kumar said the allegations against Jay Shah were "foisted falsely".
"Congress does not have any issue and so is out to tarnish the image of Amit Shah. Instead, they should give a clarification on son-in-law model of doing business," Uttar Pradesh Minister Siddharth Nath Singh said.