For the conservation of endangered animals to be effective, information on population distribution and abundance requires regular updating from census efforts. The Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis) has recently been reclassified as critically endangered (CR) due to a rapid decline in abundance. Baseline measures currently used for identifying extinction risk and implementing conservation actions may lag behind the actual demographic trend of a population and, thus, should be updated frequently. In this study, we report the results of a line transect survey of porpoises conducted in the middle and lower reaches of the Yangtze River in 2012. Five hundred and five porpoises (95% CI = 348−662, CV = 15.86%) remain in the main stem of the Yangtze River, mostly concentrated between Ezhou and Zhenjiang. Our results reveal that the decline in the Yangtze finless porpoise population is more rapid than previously estimated. The porpoise distribution has become more restricted and fragmented with two new gaps in their distribution. We show that the extinction risk for the Yangtze finless porpoise population has increased substantially and, hence, the expected time to extinction has moved closer. Current conservation methods are insufficient and ineffective, and need to be revised. More active conservation actions, such as enforcing year-long fishing bans in the in situ reserves and building more ex situ reserves, should be implemented urgently.