The senior BJP leader made the statement when asked about the political uncertainty in neighbouring Tamil Nadu.
AIADMK General Secretary VK Sasikala had earlier written to the Tamil Nadu Governor over the "delay" in inviting her to form the government.
"When you are writing to the Governor, nobody should attribute motives to him. He is behaving in the most non-partisan manner and doing his duty," he said.
Naidu was speaking to reporters on the sidelines of The Huddle-- an event by The Hindu-- here.
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Naidu said the outcome of the ongoing intra-party turmoil in AIADMK can only be decided by the party and its leaders.
He also sought to clarify that it was not because of BJP that O Panneerselvam had resigned.
"The fact is that Panneerselvam was elected as the Chief Minister during madam's (Jayalalithaa's) period also. Subsequently, AIADMK leaders themselves have made him the Chief Minister. I am not his advocate to explain on his behalf," he said.
Naidu also clarified that BJP has no member in the Tamil Nadu assembly and there was no chance for the party to form a government there.
He said BJP does not want to fish in troubled waters of Tamil Nadu politics and dismissed as "unfair criticism" the allegation of interfering.
"We are not preparing any ground. It is their internal matter. Both the AIDMK General Secretary and Chief Minister Panneerselvam are making statements. We don't want to fish into the troubled waters," he said.
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