Khanna in a Facebook post said that he has sent his resignation to the Speaker of the State Assembly. He, however, did not clarify whether he will resign from the primary membership of Congress.
In the post, he said the time has come for him "to step away from politics."
On speculation of joining SAD, Khanna said he did not do so as Amarinder Singh was announced Congress nominee for Amritsar Lok Sabha seat and his decision would have had adverse effect on the former Chief Minister's prospects.
According to party sources, Khanna was upset over Sangrur MP Vijay Inder Singla allegedly ignoring him and other senior leaders of Assembly segments while distributing MPLAD funds and launching development projects.
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Singla has sought re-election from Sangrur parliamentary constituency.
Khanna was also unhappy after Patap Singh Bajwa was elected as PPCC chief, party sources said.
In the 117-member Punjab Assembly, the strength of Congress is now reduced to 43. SAD has 57 members while its ally BJP 12 and there are three Independents.