The Southern Metropolis Daily, citing an internal Ministry of Railways report, said cracks had been detected in tunnels, some of which had been built without the steel bars needed to reinforce them.
Wiring at the Wenzhou South Station, which is on the line where the deadly bullet train collision took place in July last year, was also discovered to be substandard.
At least 40 people were killed and hundreds injured in the July 2011 accident, which has since been blamed on design flaws and poor management.
It followed the dismissal of former railways minister Liu Zhijun in February 2011. He is facing prosecution for corruption after reportedly taking bribes of more than 800 million yuan during his time in office.
China’s high-speed rail network, the largest in the world, has been plagued by graft and safety scandals following rapid expansion.
The Southern Metropolis Daily, which has a reputation for its outspoken reporting, said the railways ministry had ordered “complete correction” to the shortfalls by certain deadlines that should “leave no more potential risks”.
The ministry did not immediately comment on the report when contacted by AFP.
In March, a section of a new high-speed railway in central China’s Hubei province collapsed following heavy rainfall.
Opened to passengers only in 2007, the high-speed rail system grew rapidly thanks to huge state funding and had 8,358 kilometres (5,193 miles) of track at the end of 2010.
China’s state auditor said last year that construction companies and individuals siphoned off 187 million yuan ($29.4 million) in funds for the construction of the flagship high-speed railway line between Beijing and Shanghai.