A pro-Maratha social organisation, 'Sambhaji Brigade', later claimed responsibility for the attack.
Three youths arrived in a vehicle at the Saamana printing press building located at Sanpada in Navi Mumbai at around 1.45 PM. They called the guard of the press and requested him to take a letter, police said.
As the guard was approaching their vehicle, the youths got down from the vehicle, rushed towards the press building and allegedly pelted it with stones and fled, they said.
After getting information of the attack, police reached the spot and a complaint was lodged by the office-bearers at Sanpada police station.
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Navi Mumbai Police Commissioner Hemant Nagarale confirmed the incident.
Police said an offence has been registered against the culprits and appropriate action will be taken.
The Sambhaji Brigade took responsibility of the attack and condemned the cartoon published in the mouthpiece.
"We are condemning a cartoon which was published in Saamana. Shiv Sena executive president Uddhav Thackeray and Saamana's executive editor Sanjay Raut must apologise to the women of Maharashtra," the brigade's spokesperson Shivanand Bhanuse told PTI.
On Sunday, a cartoon on "silent march" was published in Saamana, which drew criticism from various political quarters.
The Marathas have been organising silent marches across the state following the Kopardi rape and murder incident, in which the victim was a member from the community.
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Meanwhile, Leader of Opposition in the Maharashtra Legislative Assembly, Radhakrishna Vikhe Patil today said the attack on Saamana office was a symbol of Maratha anger against the "derogatory" cartoon. He also urged the state government to take action against the newspaper.
"The cartoon insulted martyred soldiers and police," Patil said, adding Sena's sympathy for martyrs is fake.
The Congress leader demanded that Sena president Uddhav Thackeray should apologise to Marathas, women, police and families of the martyred soldiers.
He said the state government should stop giving advertisements in 'Saamana'.
"If it does not agree with the cartoon, the government should initiate action against the newspaper," Patil said.