In a statement published by Saamana Group, Prabhudesai said the cartoon was not intended to hurt the sentiments of any group or community, particularly the Marathas.
"Despite this, if it has hurt anybody's feelings, I am sorry for the same," Prabhudesai said, expressing regret for his creation.
He said though he was an artist, he was not a political cartoonist and he draws cartoons to give some comic relief to people embroiled in their daily hectic lives.
"However, my September 25 cartoon has found objections from a particular community for which I am sorry. This has resulted in a political controversy in which the Shiv Sena and 'Saamana' were dragged," said Prabhudesai.
The controversial cartoon took a swipe at the ongoing month-long agitations and huge protest marches by the Maratha community across the state.
Playing with words about the "silent processions" called "mook morchas", the cartoon showed a couple kissing with the caption "mooka (kissing) morcha", which enraged the Marathas in the state.
However, Bharatiya Janata Party (BJP) Mumbai President Ashish Shelar was not satisfied with Prabhudesai's statement and called upon Saamana executive editor Sanjay Raut, an MP, to publicly apologise to the Maratha community.
The Congress, Nationalist Congress Party (NCP) and leading Maratha organisations have demanded an unconditional apology from Shiv Sena President Uddhav Thackeray.
The cartoon had prompted an attack on Saamana's printing press in Saanpada, Navi Mumbai and editorial offices in Thane on Tuesday by members of the Sambhaji Brigade, a Maratha group.
In Aurangabad, a bonfire was made of copies of the newspaper and other forms of protests were held in different parts of Maharashtra even as the opposition, ruling ally BJP and the Shiv Sena engaged in a political slugfest.
Late on Tuesday night, Navi Mumbai Police Commissioner Hemant Nagrale said Sambhaji Brigade activists like Purushottam Khedekar, Amol Jadhavrao, Anna Sawant, and Manoj Akhre were booked in connection with the Saanpada incident.
On its part, Shiv Sena senior cabinet minister Subhash Desai flayed the Congress-NCP for fuelling the ongoing pro-reservations agitation among the Marathas all over the state.
"They ruled the state for 15 years, but did nothing for Maratha reservations... They created a farce of reservations which was later struck down by the courts," Desai said in a sharp reaction late on Tuesday.
He said that Thackeray has fully supported the ongoing Maratha agitation and even Sanjay Raut had backed it through his writings in Saamana, but it is the Congress-NCP which is vitiating the peaceful atmosphere.
