"It was accompanied by an offer for Nadia to call him which will not be acted on," Lim's spokeswoman Deborah Pead said.
While Henry had claimed to have called the celebrity chef several times, "Nadia's phone records will confirm she neither received nor missed a call from him".
"In my opinion his acknowledgement adds further insult to injury and one has to wonder why he even bothered," Pead said.
Henry's employer DGL Group had said it had been sent on Friday.
A representative for Lim says the apology was emailed from DGL's office manager to Lim's personal assistant.
Last month, Henry - founder and chief executive of a chemicals company - criticised My Food Bag for including a photo of Lim in their prospectus.
He referred to Lim as "Eurasian fluff" and that her photo was the reason for the company's underperforming results.
"When you've got Nadia Lim, when you've got a little bit of Eurasian fluff in the middle of your prospectus with a blouse unbuttoned showing some cleavage, and that's what it takes to sell your scrip, then you know you're in trouble," Henry said.
Meanwhile Lim is in isolation after testing positive for Covid-19.
The 36-year-old revealed via Facebook and Instagram she has the virus.
"I have Covid right now and [chef Vaughan Mabee] drops off a home-made pie for us," she wrote online.
Lim shared a short video clip showing off the creation by fellow MasterChef NZ judge Mabee, of central Otago's Amisfield Restaurant, in an Amisfield box.
A second post shows her two sons in bed and a shout-out to her other fellow MasterChef judge - Michael Dearth - for sending them his children's favourite storybooks from when they were young, she says.
It is not known, however, whether Lim's children or husband have tested positive for Covid too.
