"The relevant criticism that China's military participated in Internet hacking is to play the same old tune, and is totally baseless," the ministry said in a fax to Reuters in response to a question about the story.
According to the Financial Times, hackers apparently have had access to Register.com's network for about a year, but the attack did not disrupt or result in theft of client data.
It is not clear what the Chinese military would be looking for or what it would gain from Register.com's data.
Register.com says on its website it manages more than 2.5 million domain names, and also provides web management and design services.
State news agency Xinhua, citing a report from the National Computer Network Emergency Response Technical Team/ Coordination Centre of China, said that last year, 4,761 IP addresses in the United States controlled 5,580 Chinese websites through backdoor programmes, allowing remote access to a computer.
It did not provide an on-year comparison.
The ministry repeated the government's standard line that China is one of the world's biggest victims of hacking.
"The Chinese government has all along resolutely opposed and dealt with in accordance with the law Internet hacking and other relevant criminal activities, and the Chinese military has never been involved in or participated in any activities to steal commercial secrets online," it added.
The United States needs to "give a clear explanation" to the world of its theft of secrets and online surveillance "and not make thoughtless remarks about other people", the ministry said.
© Thomson Reuters 2015