Weak commodity prices hit shares including Shaanxi Coal, down 6% and Wuhan Iron & Steel, down almost 5%.
The fall in mainland shares hit Hong Kong's market. The Hang Seng index fell 1.7% - the fifth consecutive session of losses.
Investors were also cautious before a closely-watched report on the US labour market due later on Friday.
In Japan the Nikkei 225 index closed down 0.3% following a three-day national holiday.
Shares in troubled airbag maker Takata tumbled 8.6% after US regulators ordered it to expand recalls of faulty airbags.
In Australia shares recovered from early losses, the S&P ASX 200 closed 0.25% higher at 5,292.
Macquarie closed 0.3% lower after the lender posted a record annual net profit of A$2.06bn ($1.54bn; Â£1.06bn) for the year to the end of March.
Macquarie said the earnings growth was driven by its wealth management and retail banking operations.
Markets in South Korea are shut for a long weekend and trading there will resume on Monday.
The Shanghai Composite fell 2.8%, depressed by falling shares in Chinese coal and steel companies.