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Pupils aboard Gordonstoun’s 80ft sail training boat fell silent as they laid a wreath off the coast of Hopeman Harbour, where Philip first learned to sail as a teenager
On the shore, a lone student piper played while displaying the Duke of Edinburgh’s Coat of Arms on a banner.
It was presented to the exclusive boarding school’s pipe band by Her Majesty in 2019.
Speaking to the PA news agency, the school's current principal Lisa Kerr said Gordonstoun had provided stability after the turbulent early years of the prince's life.
She said: "When he came to Gordonstoun in 1934 as the school's tenth pupil it was a place where he found security and stability and a place where he was able to discover his true self and become the very best version of himself.
"It was somewhere that he developed his love of the sea, his love of sport, his connection with the outdoors and particularly built his focus on service to others, which is such an important part of the Godonstoun curriculum even today."
Ms Kerr said his connection to Gordonstoun was "lifelong", writing to the school in the final days of his life.
Three of Philip's children and two grandchildren attended Gordonstoun.
Ms Kerr added: "When he came to Gordonstoun as a parent or grandparent, there was no pomp and ceremony.
"There's a lovely story of how he came to one of Prince Edward's drama performances and he sat in a seat with a handwritten sign that simply said 'mum and dad'."
The headteacher said the ceremony had aimed to reflect Philip's love for the school and the area.
Ms Kerr said: "Throughout the whole of the last week we have had the opportunity to reflect on how proud we are in shaping what was important to the duke.
"We can't have large-scale gatherings at the moment, but to be able to have a smaller tribute to him which is still an appropriate scale is great.
"For us to put together this tribute felt like the right thing to do in these circumstances - it represents his love of the Moray Firth, Hopeman Harbour and Gordonstoun."
Pupils at Gordonstoun joined with people across the UK in observing a minute's silence for the duke.
Opportunities to hold official commemoration events have been limited due to coronavirus restrictions.