"I am resigning as minister. I cannot remain part of a government which has not defended my honour," Nunzia De Girolamo wrote on Twitter on Sunday.
Mi dimetto da Ministro. Non posso restare in un governo che non ha difeso la mia onorabilità http://t.co/NKDbvdT8jF— Nunzia De Girolamo (@N_DeGirolamo) January 26, 2014
De Girolamo was accused this month of exerting improper influence over the choice of health care managers in the city of Benevento in the Campania region, following revelations in the media of phone-tapped conversations in 2012.
She is the second minister to step down from Prime Minister Enrico Letta's shaky coalition government.
On Saturday, allegations of malpractice emerged against her ministry after Italy's financial police confirmed they carried out an on-site search this week as part of an investigation into the distribution of EU funds, Italian media reported.
Investigators are looking into discrepancies in the distribution of some €8.9 billion ($12.18 billion) for agricultural investment which were given to Italy from 2007 to 2013, according to the Repubblica daily.
De Girolamo, who is not currently under investigation, said in a statement Saturday that the police probe centered on a period before she took office.
While the EU determined where part of the funds were invested, the ministry was tasked with distributing the remaining capital through the AGEA coordinating company, which the government holds a 51 percent stake in, media reports said.