In Shanghai the benchmark composite index lost 0.82 percent, or 26.36 points, to close at 3,205.99 on turnover of 431.1 billion yuan (USD 67.5 billion).
However, it recovered from morning losses of more than three per cent.
The Shenzhen Composite Index, which tracks stocks on China's second exchange, dropped 3.06 per cent, or 56.52 points, to 1,790.31 on turnover of 365.4 billion yuan.
Hong Kong's Hang Seng Index, which fell almost one per cent in the morning, finished up 0.27 per cent, or 58.19 points, at 21,670.58 on turnover of Hong Kong dollars 94.47 billion (USD 12.19 billion).
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The market had rebounded in the previous two trading sessions after China cut interest rates to boost the slowing economy, a move also aimed at easing worries which have battered global markets.
"Investors took profits today, as the gains in the previous two sessions were quite strong. Investor confidence towards the market still needs to be restored," Haitong Securities analyst Zhang Qi told AFP.
The index lost 12 per cent in August after sliding 14 percent in July -- its biggest two-month fall since 2008.
"The news dragged down the prices of heavyweight securities firms," Zhang said.
Investors are watching the release of official manufacturing data for August today for further clues on market direction.
There is also uncertainty about the government's commitment to a rescue package launched after a year-long rally collapsed in June, which has included funding the China Securities Finance Corp. To buy stocks on behalf of the government.
"There is a lot of confusion about purchases of stocks by state-linked funds," Gerry Alfonso, a sales trader at Shenwan Hongyuan Group Co in Shanghai, told Bloomberg News.
In Shanghai, Citic Securities dropped 4.98 per cent to 15.07 yuan while China Merchant Securities gave up 1.30 per cent to 15.96 yuan.
China Construction Bank edged up 0.58 per cent to 5.17 yuan in Shanghai after it reported net profit for the first half rose less than one percent year-on-year to 131.90 billion yuan.
Pharmaceutical firms fell. Fengyuan Pharmaceutical dropped by its 10 percent daily limit to 10.08 yuan in Shenzhen while Shenqi Pharmaceutical Investment Management also lost 10 per cent to 23.41 yuan in Shanghai.