The Lord Lyon gave his first proclamation at Mercat Cross, with the words: “God Save the King”.
While the crowd shouted back “God Save the King”, at least one protester was heard booing and calling for a republic during the traditional event.
Reacting, Donald Maclaren, 64, of Livingston, said: “It’s very disrespectful, there is a time and a place if you want to protest, but this isn’t it.
“Somebody shouted ‘republic now’ then, when they were doing the three cheers, somebody was booing. “
Liz Maclaren, 67, also branded it “disrespectful”, adding: “The boos sounded like one person.”
One 25-year-old from the Capital, who said she did not want to be named, said: “It’s the public, it’s going to happen. It’s a public event there is always going to be someone doing something.”
Another member of the audience, who was filming the service on his phone, turned to his friend in disbelief as the jeers began.
It comes ahead of Her Majesty the Queen’s coffin’s arrival in Edinburgh later today (September 11).
The Queen’s cortege is expected to arrive at The Palace of Holyrood House at around 4pm, following a final journey across Scotland from Balmoral.
Queen Elizabeth II died at her Scottish residence on Thursday (September 8) and her state funeral is due to take place on Monday, September 19, in London.
Additional reporting by PA.