Serbia have been fined 80,000 euros (£65,000) and ordered to play a match behind closed doors following racist chanting and violence towards England's Under-21 players.
FA general secretary Alex Horne said the sanctions did not send a "strong enough message" about racism, and that the governing body will appeal against two-match and one-match bans for Steven Caulker and Tom Ince respectively.
Rio and Anton Ferdinand also criticised the sanctions on Twitter contrasting it with a 100,000 euro and one-match ban handed to former Arsenal striker Nicklas Bendtner for displaying a betting firm's logo on his underpants during Euro 2012.
UEFA's control and disciplinary body also banned four Serbian players and two coaches for varying terms after ugly scenes marred the end of the European Championship play-off in Krusevac in October.
Horne said: "We are disappointed with the sanctions levied by UEFA with regards to the racist behaviour displayed towards England's players.
"Let's be clear, racism is unacceptable in any form, and should play no part in football. The scenes were deplorable and we do not believe the sanction sends a strong enough message."
Anton Ferdinand tweeted: "Wow UEFA ain't serious with their punishment... So showin a sponsor is worst than racism and fighting!"
His brother Rio added: "Uefa are not serious at all on racism. Fines do not work at all. They have zero impact on federations/clubs/fans/players £fact.
"Uefa need to talk to this generation.....they don't seem to be up to date on this issue?? Harsh punishments needed as a deterrent £simple."
Sports minister Hugh Robertson, who had written to UEFA president Michel Platini demanding tough action for the racist abuse, also expressed his disappointment.
Robertson said: "I am disappointed in the punishment that has been handed to the Serbian FA given the widespread racist abuse that England's Under-21 team suffered that night. Racism is completely unacceptable and we need tough sanctions to help combat it."
The FA had reported the racist abuse to UEFA plus a number of other incidents.
Full-back Danny Rose, who was dismissed after the final whistle for kicking the ball away in anger, complained he had been subjected to monkey chants throughout the match and as he left the pitch.
Serbian FA secretary general Zoran Lakovic appeared to suggest that the UEFA official prosecuting the charges had also demanded tougher action.
Lakovic said in a statement: "If we take into account what the drastic proposed penalty by the disciplinary inspector Jean-Samuel Leube we have not been hit so hard.
"I believe that this is a final warning to all of us who work in Serbian football, including coaches and players and fans, because for even the smallest mistake UEFA can now impose the most rigorous punishment."
Lord Herman Ouseley, chairman of Kick It Out, condemned the sanction as "a paltry slap on the wrist", adding: "Again we haven't seen decisive action from UEFA."
Piara Powar, executive director of European anti-discrimination body FARE, said UEFA had failed to display the necessary leadership.
Powar said: "We are disappointed in the totality of the sanction handed out to the Serbian FA. The original offences warranted a more severe collective punishment than a ban on spectators for one match.
"This is a moment in which leadership to challenge discrimination is needed from all authorities. This sanction falls short of that objective.
In relation to Ince and Caulker's bans, the FA said they were surprised at the action and that the players had merely protected themselves.
Horne added: "It is The FA's vehement belief that its players and staff acted correctly in the face of provocation, including racist abuse and missiles being thrown.
"We are therefore surprised to see that two of our players have been given suspensions. We shall await UEFA's reasoning but it is our intention, at this stage, to support our players and appeal these decisions."
England Under-21 head coach Stuart Pearce added: "I am concerned to see our players suspended by UEFA and we will continue to support them. I maintain that our players played no part in the aggression. From what I witnessed our players and staff were forced to protect themselves in the violent scenes that followed the game."
Serbia fitness coach Andreja Milunovic and assistant coach Predrag Katic were both banned for two years, part of the ban being suspended for three years in each case.
Four Serbia players were also banned - Goran Causic for four matches, Ognjen Mudrinski and Filip Malbasic for three and Nikola Ninkovic for two.
Serbia and the FA have three days in which to lodge an appeal - while UEFA themselves can also appeal against the control and disciplinary body if they too think the independent commission have been too lenient.