"The killing of the father of a Bharatiya Janata Party worker has nothing to do with naming of the square after Prime Minister Modi," Mr Dwivedi said.
Two senior Bihar BJP leaders on Saturday last, however, claimed that Ramchandra Yadav, 70, was beheaded after he named a town square "Narendra Modi chowk".
"The dispute that escalated (and led to the murder) had started due to this chowk being named Modi Chowk," Bihar BJP president Nityanand Rai told reporters after visiting Darbhanga, 150 kilometres north of Bihar capital Patna.
But Union Minister Giriraj Singh, who also met the Yadav family, accused the police of trying to hide the facts of the case.
The claims by the two BJP leaders contradict those of the local police and Deputy Chief Minister Sushil Kumar Modi.
"Totally false that the murder in Darbhanga case was due to naming Modi Chowk. It was a case of land dispute. The board was put long back, murder has nothing to do with board," Sushil Modi had tweeted on Friday last.
With inputs from IANS