The eccentric entrepreneur, also head of SpaceX, backed the conspiracy theory that extraterrestrials were involved in the construction project in multiple posts on Twitter.
But Egypt's international co-operation minister rejected the claims and said the efforts were all down to human endeavour.
She added that the tombs of the pyramid builders, discovered in the 1990s, ranked as proof that the incredible structures were built by ancient Europeans.
She also invited him to check out the evidence for himself.
The tech tycoon tweeted that "Aliens built the pyramids obv", which has now been retweeted almost 85,000 times.
He added: "The Great Pyramid was the tallest structure made by humans for 3800 years. Three thousand, eight hundred years.
Egypt's Minister of International Co-operation Rania al-Mashat replied to him on Twitter, saying she followed and admired Mr Musk's work.
But she encouraged him to read more about how the structures built for pharaohs of Egypt - and to come and have a look at the tombs of the pyramid builders himself.
She wrote: "I follow your work with a lot of admiration.
"I invite you & Space X to explore the writings about how the pyramids were built and also to check out the tombs of the pyramid builders.”
There are still more than 100 surviving pyramids, with the most famous being the Great Pyramid of Giza in Egypt - standing at more than 450ft (137m).It is one of the seven wonders of the world.
It's estimated that this pyramid was made from 2.3 million blocks of rock and weighs 5.9 million tons. Scientists estimate it took at least 20,000 workers over 23 years to build it.