It is understood that Henderson and Waite decided not to return to shore, reasoning that the shark was unlikely to return to the same spot.
While Bells Beach and other popular surf spots are not far from Geelong, Henderson is among only a few Cats players who use the sport as a recreation.
Patrick Dangerfield is another notable Geelong surfer, but golf is far more popular among their players.
Henderson is expected to return from a knee injury for Friday night's preliminary final against Sydney at the MCG.
AFL players are discouraged from taking part in activities that put them in harm's way, with some risky pastimes banned outright.
Several Cats players, including star recruit Patrick Dangerfield, take to the waters along Geelong's popular surf coast during the season.
But Scott admits he could have a mutiny on his hands if he tried to stop his players catching a wave in their down time.
"I reckon I would," he said when asked if players would revolt against a ban on surfing.
"We've got a lot of surfers and it's an important part of their preparation," Scott said with a wry smile.
"So I'll just try to not to think about the sharks."
The incident provided Scott with one of the more-bizarre scenarios an AFL coach has had to deal with as he prepares his team for a preliminary final.
While several other surfers had the perfectly natural reaction of paddling madly for shore, Henderson and Waite remained in the surf.
"I was interested to hear that they stayed out there - I knew they were brave but I didn't realise they were that brave," Scott added.
"It probably suggests to me it was more likely a dolphin than a shark." No one was harmed in the incident.
- AAP
