The minister was attending the wedding ceremony of son of former minister Parameshwar Naik at Hagaribommanahalli in Davanagere.
The portfolios were cleared by Congress president Rahul Gandhi as the exercise had turned out to be tricky for the party state leaders.
The resignation letter states he is resigning as MLA of Mandya constituency, without assigning any reason.
With the cabinet expansion being deferred repeatedly, several aspirants, especially those from Congress, had openly expressed their displeasure over the delay, piling pressure on the party to fill its quota so as to avoid any trouble ahead of the 2019 Lok Sabha polls.
Nine ministers of cabinet rank and four ministers of state were inducted at the swearing in ceremony at Raj Bhavan with Governor Vajubhai Vala administering the oath of office and secrecy.
CM Siddaramaiah announced the CID probe and warned of action against the seniors accused of harassing Ganapathy.