"China is making good progress... but China is still facing serious health challenges and needs to keep working hard now and in the future," Chan told a press briefing at the end of her five-day trip here.
She said she was "impressed" with China's improvement in disease prevention and response measures after the SARS (Severe Acute Respiratory Syndrome) outbreak in 2003 that saw Beijing criticised for an initial cover-up.
After emerging in the southern province of Guangdong in 2002, SARS infected more than 8,000 people worldwide and killed more than 800.
Progress has been made in combating other illnesses including bird flu, tuberculosis, hepatitis and HIV/AIDS, she said, thanks to greater investment in the health sector.
"In recent years, China has been demonstrating growing political commitment to public health," she said.
"But 1.3 billion people live in China... many of China's health challenges can become global challenges."
She said she was satisfied that the number of outbreaks of bird flu had dropped in China.
Since emerging in 2003, the H5N1 strain of bird flu has infected at least 25 people in China, 16 of whom have died. But the most recent death was in June of this year.
"But I would like to give one piece of advice... don't let your guards off. The risk of the influenza pandemic is still with us," she said.
Chan said she met with health and agriculture officials and discussed with them a range of current health issues and emerging threats such as obesity, cardiovascular diseases and environmental risks.
She praised the Chinese government's pledge to provide its citizens with free basic health care by 2020, stressing the link between poverty and illness.
"China has come far in improving health outcome but there remains much work to do," she said.