Pressure has increased on the 29-year-old in recent weeks as his side slipped to a 1-0 defeat to Sri Lanka, which followed a disastrous winter for England when they were whitewashed by Australia in the Ashes.
However, Flower believes that the criticism Cook has faced has been unfair considering his past performances for the Three Lions.
He told The Telegraph: "It seems to be forgotten, and people should not forget, that this is a young man, a 29-year-old man, who has done some extraordinary things for his country.
"He has scored the most Test centuries for his country – that in itself is an amazing achievement, and he's got so much more left to give. He's led the one-day side for a while now and has got the most one-day wins of any England captain.
"He's led the side to an astounding Test victory in India, against the odds, and in the main on pitches which England have traditionally struggled on, and tactically he was excellent in India. If he hadn't been, we would not have won."
England begin their five-match Test series with India next week at Trent Bridge.