The governor accepted the resignations of Home Minister P. Sabitha Indra Reddy and Roads and Buildings Minister Dharmana Prasada Rao, sources in Raj Bhavan said.
The ministers submitted their resignations to Chief Minister N. Kiran Kumar Reddy on May 20 on the direction of the Congress party's central leadership.
Both senior ministers have been charged in the disproportionate assets case of the YSR Congress party leader Y.S. Jaganmohan Reddy.
The chief minister is believed to have forwarded the resignations only after getting a nod from the central leadership.
The resignations came after mounting pressure from a section of leaders within the ruling party as well as the opposition for sacking of tainted ministers.
After he was named as an accused in the fourth charge sheet filed by the Central Bureau of Investigation (CBI) in August last year, Dharmana submitted his resignation but it was not accepted by the chief minister, who also refused to give permission to the CBI to prosecute him.
Sabitha also offered to quit after she was named in the fifth charge sheet filed last month but the chief minister advised her not to do so.
Both the ministers, who had served in the cabinet of Jaganmohan Reddy's father Y.S. Rajasekhara Reddy (2004-09), have been accused of showing undue favours to companies which invested in Jaganmohan Reddy's business, allegedly on a quid pro quo basis.
Sabitha served as the mining minister in YSR's first cabinet while Dharmana held the revenue portfolio.