Huq, a banker and former research scholar of Oxford University, was appointed by the government after Yunus was forced to quit the Grameen Bank in May 2011.
"He tendered his resignation letter to the finance minister (A M A Muhith) saying he decided to quit due to 'personal reasons'," a senior finance ministry official told PTI without elaboration.
Earlier on Monday, Huq met the finance minister at his secretariat office and told reporters that Grameen Bank was now "doing well" and "I don't think there might be new initiatives" for changing the bank's existing structure, as was suggested earlier.
Huq's resignation came as Muhith yesterday confirmed that the government would not intervene in the ownership or management structure of the Grameen Bank, backtracking from a controversial plan to split the bank into 19 entities, offering the government its absolute control.
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"The government has no intention of changing the ownership or management style of the bank (Grameen Bank)," he said responding to a question after months of uproar about the planned restructuring of the Grameen
Yunus earlier in a statement said the government takeover of a sound financial institution owned by 8.4 million poor women in line with a government commission's suggestions would be a case of an "extreme abuse of power".
Yunus was forced to step down in 2011 as Grameen Bank's chief executive following his dispute with the government. Later he also lost his court battle to retain the position.
The government said Yunus had to quit Grameen as his age limited stipulated for bank managers expired but it is widely believed he earned displeasure of the government's top leadership for esoteric reasons.
Yunus's experiment of poor men's banking earned Bangladesh the repute of being the home micro credit and earned him the Nobel Peace Prize along with his Grameen Bank.