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Cyclist Andy Rolfe posted the video on social media showing the bus, in Denbighshire for the Tour of Britain, narrowly missing him while overtaking.
Sky said the driving was "unacceptable" and that drivers will be "reminded of their responsibilities".
"Encouraging people to get out and on their bikes is a huge part of what we stand for as a team," a statement read.
"We are a team of cyclists and we know how important it is for us to set an example when it comes to ensuring cyclists are able to use the roads safely."
Rolfe described the incident as "crazy" and said the video needs to be shared "for the safety of cyclists".
UK Cycling's senior road safety campaigner, Duncan Dollimore, said: "Team Sky employees should know better than most the dangers of close overtaking of cyclists."
Team Sky have apologised to an amateur cyclist after their team bus almost knocked him over in Wales.