Senior IAS officer Alapan Bandyopadhyay was appointed the interim SEC.
Upadhyay submitted the resignation to Governor K N Tripathi at the Raj Bhavan.
"He (Upadhyay) came to me at about quarter to four and handed over his resignation. I received the resignation. He pressed for it and I have sent the resignation for the comment of the government. I am yet to receive the views of the government at this stage," the Governor told reporters here.
To a question whether the resignation was unfortunate, the Governor said "You can make your own comment. I should not give my comment on it. He (Upadhyay) has resigned and that is a fact."
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Soon after stepping down, S R Upadhyay told a news channel "I have resigned because I felt I must resign. There must not be any pressure from any political party to influence any decision. It is not a correct way."
The state government has forwarded the name of Principal Secretary state Transport Department Alapan Bandyopadhyay, as interim SEC.
Rruling Trinamool Congress declined to comment on the resignation of Upadhyay and appointment of Bandopadhyay as interim SEC and hoped whosoever takes over as SEC would hold the counting of votes on October 9 as scheduled.
"We don't have any reaction. He wanted to resign, he has resigned. It is his matter. We hope that whoever takes over will hold the counting of votes as scheduled," a senior TMC leader told PTI on condition of anonymity.