But Hong Kong shares rose over 1 percent, tracking rebounds in Asian markets as some fears that Britain would vote to leave the European Union abated.
Both China's blue-chip CSI300 index and the Shanghai Composite Index lost 0.2 percent, to 3,105.71 points and 2,880.08 points, respectively.
Last week, U.S. publisher MSCI decided not to add yuan-denominated Chinese shares to its emerging market index. Many watchers say the decision at least partly reflected fund managers' unease about allocating more to yuan assets.
Responding to yuan depreciation fears, the Financial News, a paper owned by China's central bank, said in a commentary on Monday that although there is no concrete basis for depreciating the yuan over the long term, more two-way volatility is unavoidable while reforms proceed.
Market sentiment was also hit by a weekend announcement from China's securities regulator that it would tighten rules on major restructurings by listed companies to curb speculation around shell companies used for backdoor listings.
Most sectors were down in China, with resources and transportation shares leading the declines.
But real estate shares strengthened after data showed China's home prices rose faster in May as smaller cities joined the rally in bigger cities.
In Hong Kong, the Hang Seng index added 1.1 percent, to 20,388.49 points, while the Hong Kong China Enterprises Index gained 1.0 percent, to 8,574.22.
Hong Kong-listed shares of Vanke lost 2.9 percent, after China's biggest developer said it would acquire a unit of Shenzhen Metro Group for 45.6 billion yuan ($6.9 billion) via a new share issue, making the state-owned subway operator its largest shareholder.
Shares of Stella International Holdings tumbled for a second session, after last week's warning of a significant drop in first-half profit.