The announcement came hours after Khan criticised the leadership of state Congress chief Arun Yadav and praised the ongoing revamping of the party in view of the 2018-end assembly assembly polls in Madhya Pradesh, where the BJP is in power since 2003.
Addressing a press meet here in the afternoon, the former Union minister said Yadav was no match to Jyotiraditya Scindia, the Congress chief whip in the Lok Sabha, and party veteran Kamal Nath, in terms of stature and leadership.
His resignation was accepted on September 13, 2016, Mishra said, adding the two-time Lok Sabha member is no longer associated with the main opposition party.
"Khan was now playing into the hands of the BJP," the Congress spokesman told PTI.
When contacted, Khan said he has not been informed that his resignation has been accepted.
"I have not been informed, either by the central leadership or the state leadership, that my resignation has been accepted," he added.
Earlier in the day, Khan told reporters 'achhe din' (good days) are in the offing for his party in Madhya Pradesh, where the Congress is in a revamp mode.
"Congress ke Madhya Pradesh me achhe din aane wale hain (good days for the Congress are in the offing) as revamping in the party has begun," he added.
The Congress central leadership recently appointed Deepak Babaria as AICC general secretary in-charge of Madhya Pradesh, replacing Mohan Prakash.
He also announced the formation of National Congress Alpsankhyak Dal, an outfit, which he said, will work towards strengthening the party in areas dominated by minority communities.
He said the BJP governments at the Centre and in Madhya Pradesh have "failed" on all counts. The youth, farmers and commoners are feeling "cheated" by the saffron party.
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