China's all-important manufacturing sector remained in the doldrums during the month of September, according to two separate reports on Thursday.

The government's official gauge of factory activity improved with the manufacturing PMI rising to 49.8, up from August's three-year low of 49.7 but still marking two straight months of decline. Meanwhile, a private survey by Caixin/Markit revealed PMI fell to a fresh six-and-a-half year low of 47.2, ticking down from August's reading of 47.3 but still better than an earlier flash estimate of 47.

A reading below 50 indicates activity is shrinking on a monthly basis, while one above indicates expansion.

Unlike the government's gauge that concentrates on large firms, Caixin's survey focuses on smaller and medium-sized companies.

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Total new work fell at the quickest rate in over three years, partly driven by a steeper fall in new export business, Markit said in a report. As a result, companies cut output at the sharpest rate in six-and-a-half years, while staff numbers fell at the quickest pace since the start of 2009

Chinese financial markets were closed Thursday for the start of a week-long public holiday, but the rest of Asian indices traded higher following the two reports. Japanese and Australian shares led gains by more than 1 percent each, while the Australian dollar (Unknown: AUDUSD=) added 0.4 percent against the greenback.

In other surveys released on Thursday, the official services PMI for September came in at 53.4, unchanged from August, while Caixin's final report showed the services index slumping to a 14-month low of 50.5.

Shortly after the reports, Markit announced it will stop releasing monthly preliminary readings of manufacturing PMI, known as the flash estimate. It will continue to issue monthly Caixin China general manufacturing PMI and general services PMI.

The official PMI tends to print higher than Caixin's since it tracks large, state-owned enterprises (SOEs), which are benefiting from government stimulus and infrastructure investment, explained Julian Evans-Pritchard, China economist at Capital Economics.

Indeed, several experts have pointed out that Beijing's monetary and fiscal stimulus throughout this year tend to be more favorable to SOEs since they have better access to bank loans than smaller, private enterprises. Moreover, officials unveiled plans for reforming SOEs earlier this month that include more public private partnership investment, a factor likely to boost those companies further.