He died peacefully at home on Sunday (February 14), surrounded by his family.
The news was shared on social media by the Clan Macpherson Museum in Newtonmore.
A post on Twitter read: “We are so very sad to share the news that our 27th Chief, Sir William Macpherson of Cluny and Blairgowrie – 'Cluny' to us all - died peacefully at home on the 14 February, surrounded by his family.
“The flag at the museum has been lowered to Half Mast in honour of his memory.”
Scotland's Deputy First Minister, John Swinney, also paid tribute to Sir William on Twitter.
Mr Swinney wrote: “Very sorry to hear of the death of my constituent, Sir William Macpherson, distinguished High Court judge, who led the Inquiry into the Stephen Lawrence case.
“The challenge, rigour and humanity of his report was a product of who he was. He did much good locally in Blairgowrie.”
Sir William was a Judge of the High Court of England and Wales (Queen's Bench Division) where he served as Presiding Judge of the Northern Circuit until his retirement in April 1996.
Before his appointment as a judge, Sir William was a Queen's Counsel practising in London and abroad.
A spokesperson for the Clan Macpherson Association, said: “We were fortunate to have had his guidance, support and leadership for an incredible 50 years and the world will have benefited from his 94 years on this earth.”