Dozens of bodies are waiting in hospital accident and emergency rooms across the global financial hub to be transported to mortuaries, said Tony Ling, head of the city's Public Doctors Association.
"These bodies now need extra time to wait for collection because resources are just so tight," due to manpower and storage capacity shortages, he said.
The government and Hospital Authority did not immediately respond to requests for comment.
There have been more than 600 coronavirus-linked deaths in Hong Kong since the start of the pandemic in 2020, less than in other similar major cities.
However, numbers are climbing daily with a record 83 deaths on Sunday. Around 300 deaths have been recorded in the past week, with the majority unvaccinated residents.
Hong Kong has a large proportion of unvaccinated elderly despite a recent pick-up in vaccinations. Many have hesitated to be inoculated due to a fear of side effects and complacency due to the city's success in controlling the virus in 2021.
Medical experts have said the city of 7.4 million residents could see cumulative deaths from the virus potentially rising to around 3,206 by mid-May.
Around 4,000 people on average die each month in Hong Kong, according to 2020 government figures.
Hong Kong has stuck firmly to a "dynamic zero" coronavirus policy which seeks to curb all outbreaks, like that in mainland China. To achieve this, the former British colony has unleashed its most draconian measures since the start of the pandemic, adding to rules that were already among the world's toughest.
The city has recorded over 171,000 infections in total, with around 160,000 of them since the start of February due to the highly transmissible Omicron variant.
The government has in recent days communicated to the public at press conferences that the deaths are mostly among unvaccinated people. Previously that information was not readily given.
Hong Kong leader Carrie Lam said mainland Chinese experts had suggested to her administration that they explain "more clearly the clinical situation of the death cases to the public and boost vaccination among the elderly", according to a government statement released on Sunday night.
Chinese officials have stepped in to bolster Hong Kong's efforts to fight the outbreak after President Xi Jinping told the city's government to make it their "overriding mission" to control a worsening Covid-19 outbreak.