The cause of the toilet paper shortage was not immediately clear, but speculation was rife on social media about possible holdups involving the supply chain in mainland China.
The city's government said late on Wednesday that it regretted that the "malicious act of spreading rumours" caused shortages of products like rice and toilet paper. It added that steps to contain the coronavirus would not affect the movement of freight across the border.
Vinda International Holdings, a Hong Kong-listed toilet paper producer, didn't immediately respond to a request for comment on Thursday, nor did some of Hong Kong's supermarket chains. Vinda shares rose as much as 8 per cent to a record high in the morning session.
One man carrying a sack of toilet paper rolls on the street on Wednesday evening said a friend had lined up to get them. Others didn't have friends to help.
Visits to eight supermarkets near the main business district by a Bloomberg reporter turned up no rolls. Two men stood outside a U Select supermarket in the Sheung Wan neighbourhood, trying to figure out how to plan their lives around having no toilet paper.
"We went to five stores and no toilet paper," said Mr Lok Gork, 30, a designer living in Hong Kong. "We got some wet wipes. You never know. You're better safe than sorry."