"He is the top most person in the country by becoming the President. I congratulate him," Hazare told reporters here.
When asked about the allegations raised by Team Anna against him, Hazare refused to answer saying, "I do not want to speak about it."
His remarks came at a time when his team levelled serious allegations against Mukherjee, who was sworn in as the new President yesterday, at the first of their indefinite fast against UPA government.
Team Anna had even masked the photograph of Mukherjee in a collage at the site in a symbolic protest.
Addressing the protesters yesterday, Team Anna member Arvind Kejriwal had said, "If Lokpal was there, Mukherjee would not have been the President. The Constitution provides immunity to President from any investigation. Now Congress has put a 'chadar' (veil) of constitution on the President."
However during his address, Hazare did not make any personal remarks against either Mukherjee, Prime Minister Manmohan Singh or any other ministers.
Team Anna had two days ago spoken in different voices on the demands of the protesters with activists saying that their stir was for three demands, including setting up of a special team to probe corruption allegations against 15 Union Ministers, but Hazare said it was Lokpal.
At a press conference two days ago, Team Anna member Prashant Bhushan said their protest is "limited" to an SIT probe against ministers, a fast track court to try cases against MPs and the SIT to go into allegations against party chiefs.
However, Hazare immediately took the microphone and said "the fight is for Lokpal Bill" and went on to add that till the 15 ministers against whom they have raised allegations are jailed if they are guilty, the country would not get a strong anti-corruption mechanism.