Marigowda has submitted his resignation to the Secretary of the Urban Development Department Deepa Cholan in Vikasa Soudha in Bengaluru.
The resignation was submitted, reportedly as per the instructions from CM Siddaramaiah.
Before tendering the resignation, Marigowda met CM Siddaramaiah at his Cauvery residence and held a brief meeting with him.
Speaking to media persons after resigning, Marigowda said: "I have resigned as my health is not good. The MUDA investigation is going on and let that continue. I won't comment on whether it is a scam or not. The investigation is underway and the truth will come out."
He claimed that there was no pressure on him to resign.
Praising the chief minister, he said: "CM Siddaramaiah is our leader and we have been together for 40 years. He had made me President of taluk and zilla panchayats. CM Siddaramaiah has never asked us to indulge in illegalities. In MUDA matter also, the CM has not exerted any pressure."
"I have suffered a stroke two times. I am not healthy. I have resigned citing my inability to continue in the post. It is also not true that the Minister for Urban Development Byrathi Suresh has pressured me to resign," Marigowda claimed.
Recently, Siddaramaiah's wife Parvathi voluntarily surrendered 14 sites MUDA allotted her.
Earlier, Marigowda was booed and asked to leave the event by the supporters of CM Siddaramaiah when he arrived to join the latter in Mysuru.
Siddaramaiah's supporters alleged that he got into trouble because of Marigowda.
The MUDA case involves allegations that the authority "illegally" allotted 14 sites to Siddaramaiah's wife, B.M. Parvati, in an upscale area of Mysuru city.