"Yoga is universally accepted, but unfortunately mired in controversy because it has been inextricably linked up with Modi politics," Gogoi tweeted.
In a series of tweets, he said yoga was good for health and "so also all other forms of physical exercises."
"However, my priority is providing nutritious food, medical care, housing, sanitation, drinking water and employment opportunities," Gogoi said.
Meanwhile, the first International Yoga Day was celebrated in many parts of the state.
While the state government organised the official function to celebrate the day at Sarusajai stadium, the Union Youth Affairs and Sports Ministry held a separate yoga session at Veterinary College Ground here during the same time.
Later, Assam Governor P B Acharya inaugurated a Youth Convention organised to mark the occasion.
"Youth are the heart and pulse of the nation. But, we must remember that a nation will remain healthy and energetic only when our youth remain healthy both in body and mind," Acharya said.