Wang Guoqiang, deputy minister of health and director of the State Administration of TCM, made the remarks on the sidelines of the annual session of the 11th Chinese People's Political Consultative Conference National Committee.
"We should keep making good use of animal-based medicines while ensuring proper animal protection, which is also in line with the country's laws and regulations," he told China Daily.
This was the first time a top health official talked about the issue after accusations of animal cruelty were made, particularly online, against a Fujian-based drug company that makes medicine from bear bile and that applied to raise funds through an initial public offering.
The protection of animals is a hallmark of a civilized society, but "the practical situation has to be considered as well", Wang said.
"So far we have found no substitute for bear bile, which has proven medically effective and is irreplaceable," he said.
Cao Hongxin, a CPPCC member and former president of China Academy of Chinese Medicine Sciences, said bear bile can cleanse the liver, improve vision and relieve muscle pain.
Powdered bear bile sells for 4,000 yuan ($635) a kilogram.
"Animal-based drugs are an important part of TCM, in addition to herbal and mineral medications, and some people who are motivated by some other agenda might use the media hype and criticism of the issue to attack TCM" he said.
TCM medicines made from animal ingredients - such as tiger bone, musk, rhinoceros horn and antelope horn - have been used for thousands of years in China, Wang added.
"It's totally correct to heed animal welfare, and we are in fact carrying out research on substitutes such as animal-based drugs, whether natural or synthetic," he said.
"It's definitely no easy job and will take a long time," he said.
Some netizens, however, thought otherwise.
"People suffering from some diseases would die without bear bile. In fact it's widely used for health preservation products," said an online writer called Halubi in a post on the Sina news portal.
According to the State Forestry Administration, China had 68 registered bear farms by 2006 where about 7,000 black bears were kept for bile extraction.
CPPCC members Feng Jicai, a famous writer, and Han Meilin, an accomplished painter and sculptor, made a proposal calling for the immediate cessation of bear bile extraction.
He called for a revision of the current regulations to outlaw the practice.
Han Meilin said: "Although I haven't personally witnessed bile extraction, I could feel the pain. It's heartbreaking."
Incensed by some claims that the process is painless and harmless for bears, Han urged in the proposal that the authorities cooperate with scientists to conduct research, and if that showed the practice harmed animals, to ban the extraction of bear bile.
"They said there is no pain because they were not stabbed. I wonder what they would say if I poked them," Han said.
"To be honest, I don't think there is any point discussing this. Consensus should be immediately reached on this issue without rehashing the previous discussion," Han said.