In a 1400-word open letter to Vettori The Times newspaper today, under the heading "Not exactly a captain's innings yet, is it Daniel?, Atherton labelled him "rude" and insisted his late arrival would have caused division in the tour squad.
Vettori and teammates Brendon McCullum, Jacob Oram, Ross Taylor and Kyle Mills were permitted by New Zealand Cricket (NZC) to miss the first week of the tour to play in the lucrative Indian Premier League (IPL).
They missed the first two matches, the one-day tour opener at Arundel and the three-dayer against Kent at Canterbury which were both rain-affected.
A cut finger then ruled Vettori out of the final warmup match against England A, leaving him short of bowling preparation.
"Can you imagine the hoo-ha if the England captain had not arrived with his team," Atherton wrote, adding it was hard to recall a captain arriving late for a major tour.
"...The end of amateurism was supposed to put a stop to all that. Maybe you would like to walk out on to the ground this morning from a different entrance, too."
Atherton reminded Vettori of his comments about the shortened form of the game at last year's world Twenty20 tournament, when he said he hoped it was "only part of the landscape and not the future of the game".
Atherton wrote: "How do the rest of your boys feel? Jealousy is never a good thing in a team sport.
"Still, it is good to know that you are more enthusiastic about Twenty20 now than you were during its inaugural World Cup."
Atherton said it was crucial Vettori was present from the start of the tour to bond with his players, with New Zealand taking a young, inexperienced side to England.
"Obviously, your decision to miss the start of the tour in favour of a format of the game for which you previously did not show much enthusiasm reflects the changing nature of the cricketing landscape.
"Not long ago an England tour would have been the summit of a New Zealand cricketer's ambition. Not any more, it seems.
"You had (NZC chief executive Justin) Vaughan over a barrel, didn't you? You left the decision to him, but really you knew that pragmatism dictated that he could not prevent you from going.
"He knows, as you do, that it is the only way of preventing more players joining the IPL and being lost to New Zealand for good.
"The captaincy of your country is like a nice cake, don't you think? There are the trimmings and the icing on top -- the fat contracts, the acclaim, the public profile -- but there is a lot of effort that is needed to make it work.
"While everyone else can just turn up and enjoy the finished product, the chef is responsible for making it edible.
"... You did not have to accept the captaincy of your country, just as New Zealand did not have to accept to play four warm-up matches.
"But to accept and then turn up with just over half a team is downright rude. Clearly, in this new world, old-fashioned manners count for little."
