The office of Nhom Mua at 50 Nguyen Khuyen, Hanoi, has not been open since November 13.
A major online shopping company based in Ho Chi Minh City is being probed due to its founder's alleged embezzlement.
The website of Nhom Mua (Shopping Group), a group coupon business, has not worked for several days.
Tuoi Tre reported that police arrived Tuesday at the company's headquarters at 139 Pasteur Street, District 3 as part of investigations into its founder and former executive director Tom Tran, an overseas Vietnamese who was forced to resign last week.
Tran has reportedly left Vietnam.
News website VietNamNet said police stepped in after the shareholders accused Tran of "less than transparent" management, which they said had caused them to incur losses.
Police have yet to release further details.
Kyle Pham, a Vietnamese-Australian who was promoted from finance director to executive director, said the company is having its entire operation checked and transactions would not be able to be conducted on its website until November 20.
Vivian Vo, the director at its Hanoi branch, told Vietnam Television she had been forced to resign, claiming she was unaware what she had done wrong.
But Pham said business will come back as normal, and customers will receive their orders, or a refund if their vouchers expire.
He also said the company's suppliers have shown up to pledge their intention to continue their affiliation with it.
There was a video posted online Tuesday showing a physical fight between company employees, which Pham said arose from a conflict between workers unhappy with the transition.
He said it has been settled.
Established in October 2010, Nhom Mua has become popular in Vietnam, drawing nearly four million hits to its website each month.
It employs around 900 people at offices in Hanoi, Ho Chi Minh City, Can Tho and Hai Phong.
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