Bower, who has previously been heavily critical of Meghan, made the unsubstantiated claim while being interviewed on GB News on the same day the Queen was buried.
The monarch was laid to rest alongside her husband the Duke of Edinburgh, who died in April 2021, during a private evening service in Windsor on Monday.
GB presenter Dan Wootton asked Bower: “Meghan – someone who, obviously, you have spent the last couple of years reporting on – she was very emotional today at the service. Was she close to the Queen?”
Bower replied: “Well, was she emotional back then? I mean, when she allegedly touched a tear, or was it the act of a Hollywood actress thinking it'd be a good gesture to suggest a tear?
“I think the only person that Meghan, I think at the moment, is crying for, is for herself – certainly not for the Queen."
Watch: Prince Harry and Meghan attend Queen's state funeral
Baroness Hussein-Ece, a Liberal Democrat member of the House of Lords, criticised both Wootton and Bower, tweeting: “Princess Diana was maligned and hounded until her death, mirroring exactly what’s happening now to Meghan Markle. This vile abuse has to stop.”
Former chief prosecutor Nazir Afzal added: “On this day... of all days... Dan Wooton and Tom Bowers could have had a 'moment of quiet reflection' instead of continuing to bully #HarryandMeghan.”
Broadcaster India Willoughby wrote: "Revolting. Night of the funeral. If Dan Wootton and GB News don’t like you, you’re probably a nice person."
Harry and Meghan have in recent years received critical coverage in parts of the British press, which he has described as "toxic".
Former BBC editor Jon Sopel also slammed the coverage the couple received during the royal mourning period.
He told MSNBC: “I think some of the coverage about Meghan and Harry has been bitchy and unpleasant.
"They’ve had to accept some humiliation, but they do look like they're second tier, sitting in the second row [at the funeral] behind other members of the royal family."
In July, Bower released the unauthorised biography Revenge: Meghan, Harry And The War Between The Windsors, which included controversial claims.
But some of those quoted in the book said he made inaccurate claims about the duchess.
Despite a turbulent relationship over the past few years, the Duke and Duchess of Sussex and other Royal Family members have been united in grief after the Queen’s death.
Although the duke has stepped back from royal duties and was not permitted to wear uniform on Monday, he took his place alongside his brother the Prince of Wales during their late grandmother’s state funeral.
Harry and Meghan also joined the group of royals who made their way to Windsor and took part in the committal service and interment.