Gandhi, who had publicly called the ordinance to protect convicted MPs and MLAs from immediate disqualification as complete nonsense causing tremors in the government, however, expressed his "greatest admiration" for the Prime Minister's leadership in extremely difficult circumstances.
Congress made the letter public hours after Gandhi made the comments attacking the government's position and the Prime Minister had disclosed that he had received a communication from the party vice president.
It was not clear whether the letter was written before Gandhi's remarks at a media interaction or after it.
In his letter to the Prime Minister, he said, "I realise that what I feel about the Ordinance is not in harmony with the Cabinet decision and the Core Group’s view.
"I also know it would be exploited by our political opponents. You know that I have the highest respect for you and I look up to you for your wisdom. I have nothing but the greatest admiration for the manner in which you are providing leadership in extremely difficult circumstances. I hope you will understand the strength of my own conviction about this very controversial issue."