Arvind Kejriwal told reporters that Mukherjee was a candidate for the highest constitutional post and the person adorning the top offie must be "above board".
Another member Manish Sisodia also wanted the allegations to be investigated.
Team Anna had made allegations against Prime Minister Manmohan Singh, Mukherjee and 13 others last month and demanded setting up of a special investigation team which was rejected by the Government.
The Prime Minister had last month strongly rebutted Team Anna's allegations and offered to quit public life and face any punishment if charges on coal block allotments made by the activists were proved.