The virus is expected to heap more pressure on the former British colony, which on Monday reported its economy contracted for the first time in a decade in 2019.
The alliance has threatened to step up its action, with more than 6,000 essential personnel joining the strike on Tuesday if the government refuses to respond by 6 p.m. on Monday.
Without being able to visit factories and offices, credible auditing will be impeded but the gains are far outweighed by the health risks from the epidemic which has been confirmed to infect 7,771 individuals and cause 170 deaths in mainland China.
The coronavirus epidemic, which emerged in the central Chinese city of Wuhan in December, has rekindled memories in Hong Kong of a 2003 outbreak of Severe Acute Respiratory Syndrome (SARS), another coronavirus that began in China and killed almost 300 people in the city.
Hong Kong's leader Carrie Lam has announced that 10 of the 13 border crossings with mainland China have been suspended in a bid to curb the spread of coronavirus.
Public hospitals now only have "limited number of staff on duty" to provide emergency services, while specialist outpatient clinics can only provide "limited services".
On Wednesday, dozens of medical representatives, including HAEA President Winnie Yu, marched to government headquarters to demand that the border be sealed.
"Medical worker Tracy Pui, who queued up with colleagues to sign a petition in support of the HAEA said: "(We) hope that these strikes will make the government respond to our five demands, most importantly to stop the spread of the coronavirus in Hong Kong.
Overnight, police fired teargas and rubber bullets to disperse a crowd in the city's rural New Territories after protesters denounced the government's refusal to seal the border.
Separately, a cruise ship denied access to the southern Taiwanese port of Kaohsiung docked in Hong Kong, with all passengers and crew undergoing health checks, Cable TV reported.