Amit Shah said the Sena's demands, including rotational chief minister, were "unacceptable" to the BJP.
Shiv Sena leader Sanjay Raut suggested on Thursday that Amit Shah had not informed Prime Minister Narendra Modi about the "50:50" deal between the allies and that had the BJP chief done so "in time", Maharashtra would have been spared the current government formation mess.
Sanjay Raut wondered if PM Modi was "kept away" by top BJP leaders from the decision taken over seat-sharing.
He made the comments a day after Amit Shah said the Shiv Sena's demands, including rotational chief minister, were "unacceptable" to the BJP. The Home Minister had also rejected Sena chief Uddhav Thackeray's claim that the BJP agreed to share the chief minister's post, saying that it had been said multiple times during the campaign that Devendra Fadnavis would again head the government if the BJP-Shiv Sena alliance won a majority.
Mr Shah said this had been made clear by Prime Minister Modi many times and he had also said it during the state election campaign "at least 100 times".
News agency PTI quoted Sanjay Raut as saying, "Had Shah informed Prime Minister Narendra Modi about this decision of '50:50 formula' in time, we would not have been facing this situation today."
The Shiv Sena leader also said he had heard BJP leaders talk while campaigning about Devendra Fadnavis continuing as chief minister, but did not object as he did not think it was directed at the Sena.
"I heard Modi saying that Fadnavis will continue as the chief minister of Maharashtra, but we maintained the decorum and did not object it as we did not see it as a political message to us," said Mr Raut, according to PTI.
"I wonder whether Modi was kept away by top BJP leaders from the decision taken between the BJP and Shiv Sena over seat-sharing." the Rajya Sabha member was quoted as saying.
Mr Raut said Mr Shah and Mr Thackeray had met at the Sena chief's home "Matoshree" in Mumbai in February, before the national election.
"It was the drawing room of late Balasaheb Thackeray, but for us it is a temple. The talks were held in the temple. If someone says no promises were made, it is an insult of the
temple, Balasaheb Thackeray and Maharashtra," Mr Raut said.
Amit Shah, in a statement on Wednesday, did not elaborate on the details of the BJP's pact with the Shiv Sena before the national election, saying it was not the BJP's ethic to bring to the public what has been discussed in private.
"When a promise made behind closed door is not kept, then only it comes out. We never trade in politics nor do we see politics from the angle of profit or loss. We are making it public because
it is about our self-respect," Mr Raut hit back.
President's rule was imposed in Maharashtra on Tuesday after Governor Bhagat Singh Koshyari sent his report to the centre that no party could form a government.
The BJP and Shiv Sena, allies for 30 years, won a comfortable majority together in last month's polls, winning 105 and 56 seats in the 288-member
Assembly.
But the BJP refused to accept the Sena's demand for sharing the chief minister's post for half the term. The Congress and Sharad Pawar's NCP won 44 and 54 seats.
(With inputs from PTI)