The survey team will trace the porpoises using sonar system along the middle and lower reaches of the river, collecting data on the species' population, which will assist in the making of future protection policies.
The initial results of the survey will be published in December.
"As the flagship species in the Yangtze, finless porpoises are the barometer of the river's ecological conditions," said Wang Kexiong, deputy commander of the survey team.
Scientists say the survey may not produce optimistic results, as human activities and water pollution have pushed the species to the brink of extinction.
A 2010 WWF report blamed illegal fishing, inadequate water conservancy facilities and pollution in the Yangtze, China's busiest waterway, for the declining number of porpoises.
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