Rupani said he has directed officials concerned to take strict action against those responsible for the incident.
"Chief Minister Vijay Rupani has condemned the attack on the convoy of Rahul Gandhi. The chief minister also instructed the officials to take stern action against the persons responsible for the incident," a government statement said tonight.
On Gandhi's visit to villages in flood-hit Banaskantha district today, Rupani said it was a "photo-op exercise" and dubbed Gandhi a "perpetual tourist".
"The perpetual tourist, Shri @OfficeOfRG came to Gujarat but the people of Gujarat are asking--where are our INC MLAs in this crucial time?" Rupani said in a tweet, referring to the 44 MLAs of the Congress who are putting up in a resort in Bengaluru ahead of the Rajya Sabha polls.
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"Rahul Gandhi's leadership style is working wonders in his party. Following him, Congress MLAs are also in vacation mode!" the CM said in another tweet.
"People of Gujarat know the tricks of Congress rather too well. Their anti-people and Anti-Gujarat mindset is not a secret," he tweeted.
In the Dhanera incident, a man hurled a cement brick at Gandhi's car, damaging its rear glass pane.
Earlier, the Congress vice-president was heckled by protesters at an event.
He left the stage in a huff after making a brief speech in the Lal Chowk area of the town after protesters showed black flags to him.