The former Top Gear presenter's apology to the couple yesterday over his column last year in which he said he "hated" Markle was criticised by Ed Balls and Harry and Meghan themselves.
But Morgan – the most vocal critic of the royal couple – has defended Clarkson's apology but not his original column which appeared in The Sun on 16 December.
On his TalkTV show Piers Morgan Uncensored, the former journalist said: "What happens with these two if you do apologise to them? It’s quite interesting, isn’t it?"
He also addressed Clarkson's apology: "One person who’s made a very grovelling apology today, publicly, is Jeremy Clarkson, whose now infamous column on Meghan sparked an avoidable and predictable backlash."
Watch: Jeremy Clarkson issues apology to Meghan and Harry
Morgan continued: "All columnists have had them, I’ve had them myself. But he issued a long mea culpa on his Instagram, a long one, expressing his deep, deep profound regret. But it wasn’t enough."
He went on to criticise Prince Harry's response to the apology: "Harry’s spokesman immediately hit back, ‘It’s clear this is not an isolated incident shared in haste but rather a series of articles shared in hate.’
"Again, the irony. A series of articles shared in hate. Does that remind you of anything? Does that remind you of a book called Spare spewing hate at the Royal family? You can stick you apology, Harry, where the sun don’t shine."
A spokesperson for Harry and Meghan had responded to Clarkson's apology by saying: "While a new public apology has been issued today by Mr Clarkson, what remains to be addressed is his long standing pattern of writing articles that spread hate rhetoric, dangerous conspiracy theories, and misogyny."
They added: "Unless each of his other pieces were also written 'in a hurry', as he states, it is clear that this is not an isolated incident shared in haste, but rather a series of articles shared in hate."