The governing body have also hit out at the bans imposed on Ince, Caulker and Rose on account of the events in the Euro 2013 qualifier adding that they intent to appeal
A number of England players and coaches were invovled in a mass brawl after the final whistle in the Euro 2013 play-off second leg, which confirmed the Young Lions' qualification for the Israel-based competition.
Uefa subsequently banned two of the Serbia coaches and four players, as well as handing them a £66,000 (€80,000) fine and ordering the FA to play one match behind closed doors.
However, the FA have reacted to what they see as punishments that do not fit the crime in a statement on their official website.
FA General Secretary Alex 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."
The FA also expressed their disappointment in the one- and two-match bans handed to Tom Ince and Steven Caulker, as well as the upholding of Danny Rose's suspension for their part in events in Krusevac.
The players will miss the opening game of their Euro 2013 campaign - versus Italy - and Caulker is set to be forced to watch the second group game against Norway from the sidelines as well.
Horne continued: "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.”
Head coach Stuart Pearce reiterated his belief that his players and coaching team were innocent victims, adding: "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.”
The FA confirmed they will await the written reasoning from Uefa before proceeding but suggested they will appeal the sanctions handed to their players.