Newcastle are to demand a change to the disciplinary rules after Wigan's 21-year-old forward Callum McManaman escaped any action for his studs-up challenge on Magpies defender Massadio Haidara.
The FA confirmed that the incident was seen by at least one of the match officials - even though referee Mark Halsey was unsighted - and under current rules that means retrospective action cannot be taken.
The announcement led to a storm of criticism from former players and pundits.
Newcastle's managing director Derek Llambias said the club would make immediate moves to change the disciplinary process.
To further infuriate the Magpies, assistant manager John Carver has been charged with misconduct by the FA, along with and Wigan coach Graham Barrow, following a clash at half-time in Sunday's match.
Haidara suffered potentially serious knee ligament damage after the challenge by McManaman, but no action was taken against the Wigan player during the match.
Llambias said in a statement: "We are disappointed to learn that the FA is not going to charge the Wigan player.
"It is clear from this decision that the current disciplinary procedures are not fit for purpose.
"Newcastle United, along with other clubs, have had players suspended for incidents reviewed after the game. Whilst not trivialising these incidents, they were not, in our opinion, of the seriousness of Callum McManaman's tackle on Haidara.
"Whilst we understand that the current procedures give the FA limited options, it cannot be correct that the most serious offences - those which have the potential to cause another player serious harm - can go unpunished, even if the original incident was seen by match officials.
"We will now be making a strong representation to the FA and the Premier League to see how a more appropriate, fair and even-handed disciplinary process can be introduced at the earliest opportunity to prevent incidents of this nature going unpunished in the future."
The FA's rules follow a decision taken last summer - after consulting with the leagues, PFA and referees - limiting retrospective action to off-the-ball incidents unseen by match officials unless they are exceptional circumstances.
The FA said in a statement: "In the case of Callum McManaman, it has been confirmed that at least one of the match officials saw the coming together, though not the full extent of the challenge. In these circumstances retrospective action cannot be taken."
Haidara had a scan on Monday and will have another one next week to assess the extent of the damage.