Angry MNS workers burnt effigies of Deputy Chief Minister Ajit Pawar and blackened his posters in some parts of the city.
Incidents of stone throwing were also reported from city suburbs including Chembur, Kurla and Bandra, police said.
In Thane's Ambernath, MNS workers attacked NCP office and tried to enforce a bandh today.
However, NCP spokesman Mahesh Tapase, whose office was targeted in Ambernath around midnight, claimed his party workers foiled attempts by MNS men to enforce a bandh.
Minor clashes were reported between activists of the two parties but there was no official confirmation.
Some vehicles were also damaged by MNS supporters.
Suspected NCP workers had hurled stones at Thackeray's convoy at Bhingar in Ahmednagar district and waved black flags last evening when MNS boss had gone there for some party-related work.
NCP activists were furious at Thackeray's criticism of Pawar, nephew of party supremo Sharad Pawar, whom the MNS leader blamed for the severe drought in several parts of the state.
Thackeray had at a public meeting in Solapur recently attacked Pawar, who headed the water resources ministry between 1999 and 2009, for allegedly having failed to check water scarcity despite huge spendings on irrigation projects.
There have been allegations of a Rs 70,000 crore scam in the irrigation department, which has been with NCP since inception of Congress-NCP government in Maharashtra in 1999.
Meanwhile, MNS MLA Ram Kadam issued an open threat to NCP leaders and workers if they continued to target Thackeray.
"We know how to give tit for tat. We believe in replying in the language people choose to speak to us. They (NCP leaders) have forgotten that they have to move in Maharashtra.... Their homes are in Mumbai," he said while speaking to a TV news channel.
MNS leader in the legislative assembly Bala Nandgaonkar blamed NCP for the incidents.
"Raj saheb is on a state-wide tour (during which) he is bound to criticise the government and his opponents. Raj saheb targeted Ajit Pawar and he also responded. Such criticism is nothing new. However, throwing stones at our leader's convoy and women workers getting hurt in police lathi charge is simply not done," he said.
On the attack by his partymen at NCP office in Ambernath, Nandgaonkar said MNS workers had merely reacted to the action of the ruling party. "It is up to them to stop. Our's was a reaction to their action," he said.
Shiv Sena spokesman and Rajya Sabha member Sanjay Raut said since the Home portfolio was with NCP, it was its job to prevent violence and maintain peace.