He sent the resignation letter though fax this morning a day before being inducted into Modi's Cabinet on Sunday.
Earlier in the morning he had a meeting with Goa Deputy Chief Minister Francis D'Souza who has staked claim for the CM's post.
He has claimed support of more than 12 legislators.
Reports say state Health Minister Laxmikant Parsekar emerged as the front runner for the post.
Sources have told ABP News that 17 out of 21 MLAs have registered protest against Parsekar's name.