The 60-year-old TV and radio presenter - who has hosted This Morning with wife Ruth Langsford on Fridays and during school holidays since 2006 - claimed he worked freelance for ITV, but a tribunal ruled he was effectively employed by the network.
A spokesperson for Holmes said in a statement to ContractorCalculator: “Eamonn has always considered himself a self-employed freelancer and has never knowingly avoided paying taxes. He is taking the time to understand the extensive document detailing the outcome.
“Like many people across the country and from many different professions, he is seeking to comprehend what this means; and simply wishes for clarity and consistency across the guidelines so that people don’t suffer the same confusion over these retrospective IR35 rulings.”
The former GMTV and Sky News Sunrise presenter was paid for his work on This Morning via his company, Red, White and Green Limited.
But tribunal Judge Harriet Morgan concluded that there was sufficient mutuality of obligation (MOO) and, “at least a sufficient framework of control to place the assumed relationship between ITV and Mr Holmes in the employment field”.
Holmes is consulting with his lawyers before he makes a decision to appeal the ruling, which applies to the 2011/12 and 2014/15 tax years.
Holmes, who received an OBE in 2018, has previously said he was a “test case” in HMRC's crackdown on freelance workers, claiming if they won against him they would “go after everyone else.”
He said: “I was in a court in central London for a week in June. I've been freelance for 28 years and that's been okay.
“Now they've said it's not okay. They have reinvented the rules in the past couple of years. There is nobody more freelance than me, but they are trying to prove our jobs are regular and guaranteed. They could go at any moment.”
As well as his current presenting role on This Morning Holmes hosted a weekly radio show on TalkRadio from January 2018 to February 2020. He and wife Langsford also wrote a joint coumn for Best magazine.
Last year Lorraine Kelly dodged a £1.2million tax bill for her ITV work after a judge ruled she’s performing “the role of a friendly, chatty and fun personality”, rather than appearing as herself.
The HMRC has pursued other stars over the use of personal service companies and former BBC Look North presenter Christa Ackroyd lost an appeal and was ordered to pay a £420,000 tax bill.
Yahoo UK has contacted Holmes’ representatives for comment.