Transportation Command only noticed 10% of breaches on its systems.
The US senate has accused China of attacking American airlines and military contractors more than 20 times in a single year.
Only two of these intrusions were noticed by Transportation Command, which provides transport for the American armed forces, a fact that may be due to a reported lack of communication between government bodies.
Carl Levin, a senator for Michigan, said: "These peacetime intrusions into the networks of key defence contractors are more evidence of China’s aggressive actions in cyberspace.
"Our findings are a warning that we must do much more to protect strategically significant systems from attack and to share information about intrusions when they do occur."
China denied the allegations, which are only the latest in an ongoing dispute between the two powers over cyber subterfuge.
The breaches that occurred between June 2012 and June 2013 were linked to an advanced persistent threat (APT), a type of attack that targets specific organisations over a sustained period.
Thirty other intrusions into contractors associated with Transportation Command occurred during the same timeframe, but were not attributed to China.
"It is essential that we put into place a central clearinghouse that makes it easy for critical contractors, particular those that are small businesses, to report suspicious cyber activity without adding a burden to their mission support operations," said Jim Inhofe, senator of Oklahoma.