Modi on Tuesday alleged that his chopper was deliberately delayed by the Delhi air traffic control when he was about to leave for an election rally in Bareilly.
Chouhan, however, attacked Congress party, saying it should not stoop to such tricks.
"Narendra Modi's chopper was not given clearance to fly in Delhi, two hours were wasted there. After that he had a public meeting in Bareilly, he waited inside the helicopter for 40 minutes because it was not given permission to fly," he said.
" If Congress party is thinking that by stopping Narendra Modi's helicopter, they can stop his journey to success, it is a false presumption. Bharatiya Janata Party's and Modi's journey to success cannot be stopped. Congress party should not resort to such tricks," he added.
Modi, who arrived late for the rally due to a delay, alleged that there was a conspiracy behind it.
"I want to apologise for coming late. There was two hour delay in Delhi. Then, my chopper was not allowed to take off for over three hours in Bareilly. I want the Election Commission to investigate," he said in Bareilly.
"It is pretty evident that the Congress has even lost the ability to digest their certain defeat. They are so much scared because their efforts to stop the BJP have been unsuccessful. They stooped to this level so as to cause inconvenience. The elections will go on for around 2 months. They are misusing the government for causing problem to the opposition," he added.