Players guilty of violent conduct or involved in off-the-ball incidents will be punished retrospectively even if match officials saw the incident.
Prior to this season, subsequent action could not be taken if a match official had seen an incident - no matter how poor their view of it was.
The FA tried to address this by adopting a rule change in the summer.
But new changes, which come into force on 22 November, will further tighten the FA's disciplinary regulations.
It will mean the FA can take retrospective action for violent conduct and off-the-ball incidents regardless of whether they are seen by match officials.
Fulham's Sascha Riether was the first player charged retrospectively under the initial changes to regulations governing 'not seen' incidents.
The latest changes cover "acts of violent conduct that occur secondarily to a challenge for the ball" and "in off-the-ball incidents where one or more match official did see the players coming together, but the match officials' view was such that none of them had the opportunity to make a decision on an act of misconduct that took place within that coming together".
FA director of governance Darren Bailey said: "This enables the FA to consider acts of violent conduct, like an elbow or a stamp, which have occurred after a challenge for the ball or coming together of players.
"It is sometimes difficult for officials to see such incidents, as they are often concentrating solely on the challenge for possession of the ball, and we are mindful of this.
"Also, where off-the-ball incidents are concerned, the policy adjustment will allow action to be taken where an act of misconduct could not have been seen by the match officials, even though they may have seen some part of the players coming together.
"This is an important step forward for the game and provides an appropriate level of discretion for The FA to consider action.
"However, we remain of the view that the best outcome for all is that referees are able to make correct judgements on the day to benefit the teams involved."
FA chairman Greg Dyke expressed his dissatisfaction with the current rules in October. He said: "It is understandably baffling to everyone and must be addressed.
"As FA chairman I don't like being in a position where I can't explain why we can't take action."