Micro, small and medium enterprises Minister Virbhadra Singh resigned on Tuesday after a court in Shimla framed corruption charges against him and his wife.
"I have submitted my resignation to the Prime Minister," the veteran Congress leader said after calling on Manmohan Singh at his official residence in New Delhi.
The Prime Minister has accepted the resignation and forwarded it to the President, officials said.
The Congress on Tuesday defended Virbhadra Singh saying his guilt was not proved. The party expressed hope that the former Himachal Pradesh chief minister will come out clean and face political adversaries effectively.
"He has taken moral responsibility. The matter is in the court. A chargesheet has been filed but that does not mean his guilt has been proved," Congress media department chief Janardan Dwivedi told reporters.
"I hope he will come out of it clean and face his political adversaries effectively," said Dwivedi.
Virbhandra Singh said he would return to Himachal Pradesh, his home state, "to strengthen my party ahead of the forthcoming (assembly) elections.
"I will fight it out both at the grassroots and in courts," he added.
A Shimla court Monday framed charges of corruption against Virbhadra Singh and his wife Pratibha Singh in connection with a 23-year-old case.
The former chief minister of Himachal Pradesh accused the Bharatiya Janata Party (BJP) government in the state of vindictiveness.
"It has tried to register false cases against me earlier too," Virbhadra Singh said. "In the past I have come out clean. This time also I will come out clean."
The case against Virbhadra Singh pertains to a CD from 1989 which allegedly shows him, when he was chief minister, and his wife demanding a bribe to allow investment in Himachal Pradesh.