Mainland indices erratic
China's Shanghai Composite index nosedived in the afternoon session, after fluctuating between gains and losses following the release of manufacturing data.
The Shanghai bourse finished 5.23 percent lower, while the blue-chip CSI 300 index plunged 4.9 percent. The smaller Shenzhen Composite closed down 4.8 percent and the start-up ChiNext board eased 4.3 percent.
"I feel the more plausible reason is the lack of updates on the potential stamp duty cut and initial public offering (IPO) suspension, as supportive initiatives for the recent stock market slump. Given the flighty and impatient nature of retail investors, the silence on more action could have prodded them to pare risks in the equity markets," Bernard Aw, IG's market strategist, wrote in a note.
"The persistent fall in margin debt may also have contributed to the pullback," said Aw, adding that outstanding margin lending on the Shanghai Stock Exchange fell for a seventh-straight day on June 30 to 1.34 trillion yuan.
Hong Kong markets are closed for the Special Administrative Region Establishment Day.
Read MoreChina PMI paints lackluster picture
Released Wednesday morning, the country's official manufacturing purchasing managers' index (PMI) stood at 50.2 in June, steady from the previous month and just above the 50-mark that that separates growth from contraction, data showed on Wednesday. A Reuters poll had expected a figure of 50.3. The final HSBC PMI, which focuses more on small and medium sized firms, came in at 49.4 last month - below a preliminary reading of 49.6 but above the 49.2 recorded in May.
Meanwhile, growth in the mainland's services industry picked up pace in June, according to government data. The non-manufacturing PMI rose to 53.8 from May's 53.2, adding to signs of improvements in the world's second-largest economy.