But Jyllands-Posten’s editor, Jacob Nybroe, said the cartoon, which shows the Chinese flag with what resembles viruses instead of the normal stars, was not intended “to mock or ridicule China”.
China has confirmed more than 4500 cases of a new virus, with more than 100 deaths.
Most have been in the central city of Wuhan where the outbreak began in December.
The Chinese Embassy in Copenhagen expressed its “strong indignation” and said the cartoon printed on Monday “is an insult to China”.
It added that the drawing “crossed the bottom line of civilised society and the ethical boundary of free speech, and offends human conscience.”
Nybroe told AP his newspaper “can’t apologise for something we don’t think is wrong ... As far as I can see, there are two different types of cultural understanding here.”
Danish Prime Minister Mette Frederiksen said freedom of expression in Denmark includes cartoons.
“It is a well-known Danish position, and we will not change that.”
In September 2005, Jyllands-Posten published 12 cartoons showing the Prophet Muhammad, sparking global outrage and violent protests from Muslims.
In Islam, any depiction of the prophet is regarded as blasphemous.
One of the cartoonists was assaulted.
The newspaper said it had wanted to test whether cartoonists would apply self-censorship when asked to portray Muhammad.