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The 59-year-old Christchurch man was out checking fishing nets when he got into trouble.
He was reported overdue about noon on Saturday when he was expected to return a couple of hours earlier.
His kayak was found about 2.30pm near Kaitorete Spit.
Police said on Monday night due to the amount of time that has passed, they believe they are now searching for a body.
“While no one was with him at the time, police believe he has come out of his kayak, which has then been pushed away by the prevailing wind.”
No formal searches were conducted on Monday but aerial and water-based searches of the lake are expected to resume today.