Workers of Sri Rama Sene, Hindu Janajagruthi Samiti and Hindu Mahasabha staged the protests in the districts.
Addressing the protesters at Lalbagh here, Hindu Mahasabha state convenor Dharmendra alleged that the seer's action was being used by political parties and there was a conspiracy behind this at a time when state assembly elections are around the corner.
The Swamiji's action had "deeply hurt" the sentiments of Hindus, who were always emotionally attached to the mutt, he said and asked him to step down as head of the mutt as age was catching up with him.
The Hindu Mahasabha leader also wanted to know from the BJP why they were keeping a studied silence on the issue.
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"Those who protested when Congress leader Janardhan Poojary held an Iftar at Kudroli temple here a few years back had now become mute spectators," he said.
Sri Rama Sene district secretary Prasad Ujire, who also spoke, said the Iftar had created confusion among members of the Hindu community.
In Udupi, workers of Hindu outfits held the protest in the form a puja before a makeshift idol of Lord Krishna and singing of bhajans in front of the clock tower in the town.
The Swamiji was a guru for the Hindu community and should have avoided hosting the Iftar in mutt premises, he said.
Hindu Janajagruti Samiti convenor Vijay Kumar also spoke.
Police had made tight security arrangements as a precautionary measure at the spots of the protests, which were peaceful in both the places.
They participated in the feast in the dining hall, just outside the main temple, in the event organised by Sri Vishweshateertha Swamiji. After breaking the fast, they performed 'namaz' (prayers).
The seer defended his gesture after it drew flak from Rama Sene, saying it had in no way insulted Hindus.
Sene chief Pramod Muthalik had met the seer on June 25 and announced statewide protests against him by his outfit on July 2.
He was booked on a complaint by three persons who were the seer's supporters and members of Pejawar blood donation team, police had said.