He is the second independent director to quit the company's board after the alleged fraud surfaced this month.
Already, two top level executives -- compliance officer Pankhuri Warange and Chief Financial Officer (CFO) Chandrakant Karkare -- have resigned.
In a regulatory filing, Gitanjali Gems submitted Haldipur's resignation letter dated February 14, 2018.
In the letter, Haldipur said: "Last month, my wife has undergone a major spine operation at Pune. The post operation recovery is not up to the expected level. This has resulted in restrictions on my movement. Hence travelling for board meetings at Mumbai will be very difficult for me in future.
During his tenure as an independent director, Haldipur said he received some legal notices from lawyers as well as a senior civil judge in connection with the dues from the company.
"You are aware as an independent director, I don't have a role to play in the internal working of the company and the company will take proper steps to resolve these matter," he added.
On February 14, Punjab National Bank (PNB) disclosed that it detected some fraudulent transactions with financial implication of about Rs 11,400 crore and the matter has been referred to law enforcement agencies for recovery.
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