More than 300 apps including the hugely popular instant messaging service WeChat and ride-hailing app Didi Kuaidi were infected with code potentially allowing tracking of user data, Chinese state-run media said.
The reports were a blow to the US firm, which has Greater China as its second-largest market.
Apple told AFP that it had "removed" the affected apps from its online store.
Citing US-based cybersecurity firm Palo Alto Networks, the Wall Street Journal said that the attack affected more than three dozen apps on Apple's iPhone and iPad devices.
It was not clear whether all the infected apps were Chinese.
But other firms said to be affected included Chinese ride-hailing app Didi Kuaidi, Internet portal NetEase, and mobile phone operator China Unicom, among several more.
Anti-censorship group Greatfire.Org, which tracks Chinese Internet restrictions, hacking and other online issues, said the attack appeared to originate in compromised versions of Xcode, Apple's developer software, which were then used by Chinese programmers.
"Apple notoriously manually reviews all app submissions and, in comparison to Android stores, has been relatively malware-free," it added.
Chinese authorities impose a range of restrictions on the Internet in the country, dubbed the Great Firewall, which can slow access to sites abroad to a trickle.
Many Chinese developers prefer to download software from domestic websites, Greatfire.Org said, "because of slow download speeds from foreign websites in China".
Wee Teck Loo, head of consumer electronics at Euromonitor International, added: "It is definitely embarrassing for Apple but the reality is that malware is a persistent problem since the days of PCs."
"There has been no theft and leakage of users' information or money," the statement issued at the weekend said.
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