Appearing on BBC Radio 4, Harry told listeners his fiance had a 'fantastic' Christmas at Sandringham, and that his family 'loved having' her there.
But, since that interview went live, Samantha has hit back at the 33-year-old royal and said Meghan's family 'always' supported her growing up but she was 'too busy' for them.
Samantha, who is related to Meghan through their father Thomas, lashed out on Twitter, writing: 'Actually she [Meghan] has a large family who were always there with her and for her.
'Our household was very normal and when dad and Doria divorced, we all made it so it was like she had two houses. No one was estranged, she was just too busy.
'Meg's family (our family) is complete with sister, brother, aunts, uncles, cousins, and the glue of our family, our amazing completely self-sacrificing father. She always had this family...Marrying merely extends it.
'She has a large family. She always did. Our dad is amazing and completely self sacrificing. We made it so that she had two houses. How fun it was!'
In Harry's time guest-editing the BBC program, he said: 'The family loved having her there.
'There's always that family part of Christmas, there's always that work element there as well, and I think together we had an amazing time.
'We had great fun staying with my brother and sister-in-law and running round with the kids. Christmas was fantastic.'
The part that really riled the Markle family up was when fellow BBC presenter Sarah Montague asked the royal if there were any family traditions that had to be explained to the 36-year-old Suits actress.
He replied, 'Oh plenty, I think we've got one of the biggest families that I know of, and every family is complex as well.
'No look, she's done an absolutely amazing job. She's getting in there and it's the family I suppose that she's never had.'
Meghan's mother Doria Ragland, 61, and father Thomas Markle Sr, 73, divorced in 1987 and at present Meghan's father has not met her fiance.
Samantha, whose social media page describes herself as a 'writer, a mental health counsellor and a blabbermouth', has an unknown relationship with her half-sister.
She is 17 years old than Meghan and has been the most outspoken member of the Markle family since news of Meghan's relationship with Harry began.
Samantha is also writing a 'tell-all' book about the Markle family, with the working title The Diary of Princess Pushy's Sister.
‘The title is a mockery of the media,’ Samantha told the Daily Mail in November.
‘It wasn’t me who called Meg 'pushy', it was the tabloid newspapers. She is not pushy. The book isn’t going to be negative — it’s a warm, witty, honouring book — unfortunately, the negative sing-song has gone round the world.'
Samantha even tweeted yesterday after pressed for more information on Meghan's life before Prince Harry, 'Read my book for all the fun details.'