"Was the judgement of yellow and green flags right or wrong in Brazil and why would that have to come up on a Wednesday or Thursday?" he told F1 business journalist Christian Sylt.
"That is a huge statement of a disorganised function that it should come up then," Stewart is quoted by cityam.com.
"The whole world is celebrating a new world champion and then that happens on a Wednesday. That is a poor declaration of management."
But an FIA spokesman hit back: "It was not a lack of management as there was no case to answer.
"Race control did not refer this to stewards because it was not deemed to be an incident."
Stewart, however, said the situation would be improved by replacing the system of rotating stewards at each grands prix and having at least "one man who goes to every race".
He also commented on the presidential style of Jean Todt, who since late 2009 has led the FIA in controversial predecessor Max Mosley's wake.
"I am surprised how silent Todt has been," said Stewart. "I expected him to have more presence.
"I don't know whether he's biding his time. I don't think he is by any means not smart so there must be a reason."