The major alert was sparked when a woman found the pair’s empty boat on the west side of the Isle of Lewis on Monday afternoon.
The father was rescued from the sea and taken to Ospadal Nan Eilean in Stornoway, where he later died.
A coastguard and helicopter search for his son resumed at 0400 BST.
The pair were last seen together in their Canadian-style canoe off the coast near the village of Bragar at about 1600 BST on Monday.
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The Maritime and Coastguard Agency said four coastguard rescue teams, police and a helicopter had begun searching at first light at Arnol Bay.
The search has been based on a five-mile stretch of coastline from Shawbost to Barvas. The father and son are from Arnol and would have been within sight of their home.
Stornoway Coastguard watch officer Murdo Macaulay said it was not clear what had caused the accident.
He told BBC Radio’s Good Morning Scotland programme: "We do know that when they set out yesterday they fairly rapidly got into difficulty - both of them have obviously ended up in the water and out of the canoe.
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"As time goes on now survival is becoming increasingly unlikely, I’m afraid, but there’s always hope and we’ll continue until there is no
more hope."
Mr Macaulay added that conditions were good and that the search would be reviewed mid-morning.
Local people said Monday had been a calm day but that the sea around Port Arnol was known for heavy swells and it was quite a rocky bay.
It is not known whether the pair were wearing lifejackets at the time.
Northern Constabulary said the man would not be named until next-of-kin had been informed.