Elton - who recently invited the Duke and Duchess of Sussex to stay at his holiday home in Nice, France - spoke out in defence of the couple on his Instagram.
"I am deeply distressed by today’s distorted and malicious account in the press surrounding the Duke and Duchess of Sussex’s private stay at my home in Nice last week," he wrote in the caption of a photo of Meghan and Harry speaking with schoolchildren.
The singer revealed that he and husband David Furnish had in fact provided Harry, Meghan and their son Archie with the jet to Nice.
"Prince Harry’s mother, Diana Princess Of Wales was one of my dearest friends. I feel a profound sense of obligation to protect Harry and his family from the unnecessary press intrusion that contributed to Diana’s untimely death," the 72-year-old tweeted.
"After a hectic year continuing their hard work and dedication to charity, David and I wanted the young family to have a private holiday inside the safety and tranquillity of our home. To maintain a high level of much-needed protection, we provided them with a private jet flight."
Elton also noted that their flight was "carbon neutral, by making the appropriate contribution to Carbon Footprint" to "support Prince Harry’s commitment to the environment."
The Tiny Dancer singer also commended the royal couple's "commitment to charity" and called for critics to halt the "untrue assassinations on their character that are spuriously crafted on an almost daily basis."
Ellen also took to Instagram to defend the royal couple, sharing a photo of them at the Invictus Games, with the caption:
"Portia and I met Prince Harry and Meghan in England to talk about their work on wildlife conservation. They were the most down-to-earth, compassionate people. Imagine being attacked for everything you do, when all you’re trying to do is make the world better."
After returning from their low-profile trip to Ibiza on August 12, the royal family took a private plane to Elton John's holiday home in France.
Express UK reported that their French holiday was estimated to have a carbon footprint of almost three kilograms, while their earlier trip to Ibiza was believed to have reached almost four.
The famously eco-friendly couple were slammed on social media for their hypocrisy, with Labour MP Teresa Pearce sharing the following tweet:
"Given the position they have taken publicly about being responsible on climate change, this does seem an anomaly which they should look at.
It’s up to all of us to cut our carbon emissions, and the number of flights we take a year.
That is really important — and someone as high profile as that should lead by example."