Upper Tote Cairn is situated on the shore near Loch Snizort Beag in the north of the island.
Excavations undertaken a century ago revealed the remains of a stone cist – thought to have been constructed as much as 5,000 years ago – at its base, as well as a later Viking burial chamber near the top.
Evidence with possible links to the stone age was also discovered at the site.
Duncan MacInnes, who owns the land where the prehistoric cairn stands, removed earth from the mound to use in a building project elsewhere on his croft.
The 59-year-old pled guilty to damaging the protected monument when he appeared at Portree Sheriff Court on 25 August.
On Tuesday he was fined £18,000.
Historic Environment Scotland (HES), the national agency responsible for the country’s heritage, had written to Mr MacInnes on three separate occasions about the existence of the cairn, with the most recent letter being sent in 2015.
HES officers also carried out routine site visits every ten years.
Mr MacInnes excavated part of the ancient monument between 1 and 12 December in 2018.
He was building a shed elsewhere on his property and needed topsoil.
Andy Shanks, Procurator Fiscal for Grampian, Highlands and Islands, said: “As the owner of the land this ancient monument sits on it was Duncan MacInnes’s duty to help protect it.
“Instead, he showed a complete disregard for its importance when he dug for soil and damaged Upper Tote Cairn.
“This prosecution shows how seriously the Crown Office and Procurator Fiscal Service takes these crimes, and we will continue to work with Historic Environment Scotland and other partners to make sure Scotland’s history is preserved.”
The cairn was first excavated by archaeologists in 1920.
No bones were found in the rudimentary stone cist but a large number of flints as well as fragments of charcoal were discovered, with suggestions these could have mesolithic origins.
Human remains – the end of a femur and fragments of charred bone – from a Viking cremation, interred thousands of years after the original cairn was built, were also revealed at Upper Tote.