"I read this morning they did a deal before they went in there and I think that was the suspicion right throughout the country that a deal was being done. It's disappointing."
United still have Ryan Giggs and Cristiano Ronaldo's cases stemming-from the incident on 21 September to be resolved and Ferguson said they would play things by the rules.
However, Wenger dismissed any suggestion that his club had reached an agreement with the FA. "There was no deal between us and the FA," he said.
Asked about Ferguson's comments, Wenger added: "Only the FA can respond to that. I cannot answer every opinion in the whole country. Some people are happy with the sentences we've been given, some people are not happy. For some even if you hang us it will not be enough. Maybe they wanted it at Hyde Park in front of the whole country! We cannot influence that."
Ferguson could now face a disrepute charge from the FA for his comments. This is not the first time that Ferguson has accused football officials of corruption.
In May he was fined £4,500 by UEFA for misconduct after claiming the quarter-final draw of last season's Champions League had been fixed to ensure United played Real Madrid.
Wenger also stressed that Premiership leaders Arsenal are "still considering" their right to appeal against the sentences handed out to Lauren, Martin Keown, Ray Parlour, Patrick Vieira and Ashley Cole.
Wenger said: "Why are we considering our position? Because the players have not only been suspended but they've also been heavily fined. I have a problem with both the fines and the suspensions. I know Lauren, Vieira, Keown and Parlour well and I am proud to be their manager."
Meanwhile, Ferguson said Rio Ferdinand was focusing on matches to get him through uncertainties about his future following an FA charge this week with misconduct for his "failure or refusal" to take a drugs test.
Ferguson added: "He's not enjoying it but he has managed to focus on football and that's important to him."
