The Chinese province at the epicentre of the epidemic, Hubei, reported a record rise in the death toll and health experts warned that it could worsen before getting better.
The offshore yuan and onshore yuan slid about 0.2pc each above the 6.98 level. Analysts called it a knee-jerk reaction to the new numbers on infections and death in China.
Asian currencies have responded to the virus outbreak differently.
Export-focused currencies with greater trade-linkages to China have weakened substantially, with the Thai baht dropping 4.1pc and Singapore dollar slipping 3.2pc so far this year.
However, high-yielding currencies and those perceived to be relatively insulated from economic shocks have benefited, with the Indonesian rupiah and Philippine peso fairly resilient this year.
The Singapore dollar weakened 0.2pc on the day, while the baht dipped slightly.
A senior central bank official said on Thursday Thailand's economy may grow by less than 2pc this year.
The S.Korean won depreciated 0.2pc, while the Malaysian ringgit edged down.
The Indian rupee traded 0.2pc lower. Data on Wednesday showed the country's annual retail inflation accelerated to its highest level in nearly six years, while industrial output unexpectedly contracted.
The Indonesian rupiah weakened 0.2pc to its lowest level in more than a month. It is, however, the top performing currency so far this year.
"From a growth perspective India has kind of lagged and you need an emerging economy of substantial size and growth potential and still offering decent yields. So, the IDR becomes an obvious alternative," said Mahesh Sethuraman, deputy head of global sales trading at Saxo Capital Markets.
"If risk-on assets globally are down, then we may see some IDR weakness which is more structural."
The Taiwan dollar gained as much as 0.2pc, finding some support from the government's plans to spend $2 billion to help cushion the impact on the economy from the coronavirus.