An editorial in party mouthpiece 'Saamana' said it was a "protest against mismanagement" at Maharashtra Sadan.
Shiv Sena added that the entire issue was given a "communal colour” only to derive "political mileage" and to "malign" the party's image.
"Shiv Sena respects all religions but will not tolerate if anyone tries to flaunt his religious affiliation for intimidation. One should keep his religion in his heart and in his house. But if someone wears it on sleeve and tries to malign Shiv Sena by playing politics over it, we will not tolerate it," the editorial added.
The editorial launched a scathing attack on the "poor quality of service being rendered at Maharashtra Sadan by the management".
Without naming its MP Rajan Vichare, who was seen in a video footage purportedly force-feeding a Muslim caterer, who is fasting during Ramzan, at Sadan during the protest, the editorial said, "Was it wrong to question the injustice? Was it wrong to question the catering contractor on quality of food served there?”
"What is wrong if the chapati is taken to the mouth of the contractor and he was asked to eat it. It was not written on his face that he was a Muslim. It was just a coincidence. The contractor serves such chapatis that are difficult to break. How is one supposed to eat such food?" it said.
The editorial said that basic facilities like clean drinking water, cleanliness and proper canteen management are lacking at Sadan.
"Maharashtra Sadan has become a personal fiefdom... This is an insult to the Marathi manoos. Instead of taking note of the voice raised by the Marathi MPs, the Chief Minister and the state chief secretary are trying to give communal colour to the incident," it charged.
The editorial also praised BJP MP Kirit Somaiya for "bringing to fore the corrupt practices prevalent in Maharashtra Sadan earlier."
Shiv Sena MP Rajan Vichare, who was in the midst of the controversy, defended his action, saying he had no idea about the man's religion - even though he had his name badge on.
Shiv Sena president Uddhav Thackeray had yesterday termed the uproar over the incident as an attempt to "silence" his party's voice, saying that despite being a votary of Hindutva, Shiv Sena had no hatred for other religions.
Chief Minister Prithviraj Chavan had yesterday ordered an inquiry into the complaints made by MPs regarding the services at Maharashtra Sadan.
An uproar was witnessed in Parliament on Wednesday on the issue.
While the Congress targeted the Narendra Modi government for the act, which they described as a "crime against secularism", the government first refused to comment on the issue as it involved a key ally, but seeing an angry opposition, offered to probe the matter.
Though all BJP leaders and ministers, including union Home Minister Rajnath Singh, refused to comment on the matter, party patriarch LK Advani just said "this is wrong."
But the opposition was unrelenting. Vichare's action had hurt the religious sentiments of the Muslims, MP after MP said.
Television channels started flashing a video clip shot by a local channel, which clearly showed that the first time MP Vichare was trying to force a chapati into the staffer's mouth.
The staffer was seen pleading with the MPs who were angry over the poor quality of food served at the state guest house.
Vichare and some other Shiv Sena MPs are residing at the New Maharashtra Sadan in central Delhi during their stay in the capital.
When Vichare was forcing the food into the Muslim staffer's mouth, other Shiv Sena MPs watched quietly, the video clipping showed.