Gandhi's remark came after several Union ministers came out in support of Shah's son Jay Amit Shah.
"Amazing transition from Beti Bachao to Beta Bachao," Gandhi said on Twitter, using the term "Shehzada" to describe Shah's son.
He also tagged a report headlined "Piyush Goyal defends Jay Shahs business dealings for second day" along with his tweet.
"Modiji, ...Did you act as a watchman or were you a partner? Please say something," he had said.
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The Congress has launched an all-out attack on the BJP chief with several party leaders holding press conferences across the country to hit out at Shah's son over his alleged business dealings while prodding the prime minister to speak on the issue.
The charge has been rejected by the BJP and Shah's son, who termed the report "false, derogatory and defamatory".