"What I don't accept is mainstream media immediately slapping that down as not true when they don't know it's not true," the ITV This Morning host said.
"It's very easy to say it is not true because it suits the state narrative."
He was criticised on social media and by scientists who have dismissed the theories as "complete rubbish".
"The opinions of the mainstream media or the state hardly come into the debate," said Dr Simon Clarke, associate professor in cellular microbiology at the University of Reading.
"Numerous doctors and scientists around the world have said that the disease is caused by a virus, something completely different to a mobile phone signal."
'Responsible and careful'
5G radio signals are electromagnetic waves, he explained. "Electromagnetic waves are one thing, viruses are another, and you can't get a virus off a phone mast.
"Similarly, sensible studies have failed to corroborate the claim that the signals emitted by 5G masts are able to suppress our immune systems."
Holmes made the remarks on Monday in a segment with the programme's consumer editor Alice Beer, who said the 5G theory, which has led a number of phone masts to be set alight or vandalised, was "not true and it's incredibly stupid".
He told her: "I totally agree with everything you are saying but what I don't accept is mainstream media immediately slapping that down as not true when they don't know it's not true.
"No-one should attack or damage or do anything like that, but it's very easy to say it is not true because it suits the state narrative.
"That's all I would say, as someone with an inquiring mind."
On Twitter, scientist and author Dr David Robert Grimes suggested the presenter should "talk to the scientists & physicians who are experts 1st".
Beer later reiterated her view that "the 5G conspiracy theory is nonsense and should be quashed".
A government spokesperson said: "We are aware of a number of attacks on phone masts and abuse of telecoms engineers apparently inspired by crackpot conspiracy theories circulating online.
"Those responsible for these criminal acts will face the full force of the law."
ITV declined to comment.
Analysis - Marianna Spring, BBC News specialist disinformation and social media reporter
Scientists have called the rumours that there is a link between 5G and coronavirus "complete rubbish" and a biological impossibility.
However, that has not stopped false claims being shared on Facebook, YouTube, Instagram and TikTok. Some posts have now been removed, but in recent weeks the conspiracy theory has been shared by verified accounts with hundreds of thousands of followers.
This highlights the difficulty with covering misinformation about coronavirus. A lack of information and complex explanations often fail to satisfy a desire for immediate answers.
That allows misleading information - including conspiracy theories - to thrive.