Justice Paresh Upadhyay asked the petitioners, including the author of the article Rohini Singh and founding editors of the news portal, to move the trial court to challenge the gag order.
The HC also directed the trial court to decide the matter within 30 days.
"These appeals arising from an ex-parte ad-interim impugned order of the trial court are not entertained. It would be open to the defendants to file their counter to the suit, or at least to the application for interim injunction before the trial court, if they so choose," the court said.
The HC also said that if any of the parties is aggrieved by the final order that may be passed by the trial court on the injunction application, it would be open to him to challenge it before an appropriate forum in accordance with law.
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The petitioners had sought that the interim order of the trial court be quashed and set aside as it was passed without issuing notices to the defendants, and claimed the facts did not warrant an ex-parte order.
An Ahmedabad court had last month issued an ex-parte injunction against the news portal, prohibiting it from publishing, broadcasting or printing "in any manner" programmes in any language on the basis of the article published by the website about Jay Shah "directly or indirectly" till the defamation suit has been disposed of.
Jay Shah had submitted before the high court that the appeal against the ex-parte interim order was not maintainable and deserves to be dismissed.
The petition was filed challenging the injunction ordered by a civil court on October 12 on the story carried by The Wire titled 'The Golden Touch of Jay Amit Shah'.
The lower court had issued the order against the news portal in response to a civil defamation suit of Rs 100 crore filed by Jay Shah against the reporters, editors and the company over the article which claimed that his firm's turnover rose 16,000 times in one year after the NDA came to power.
The company, according to the article, saw a huge rise in its turnover after the BJP came to power in 2014, and its revenue rose from Rs 50,000 to over Rs 80 crore in a year.
Jay Shah also filed a criminal defamation suit against the author of the article Rohini Singh, founding editors of the news portal Siddharth Varadarajan, Siddharth Bhatia and M K Venu, managing editor Monobina Gupta, public editor Pamela Philipose and the Foundation for Independent Journalism.
In his suit, he termed the article as "scandalous, frivolous, misleading, derogatory, libellous and consisting of several defamatory statements.