It is understood that Kelly will meet with senior FA officials - probably on Tuesday - and hold an investigation into the incident during Newcastle's match at Filbert Street last Wednesday.
Kelly is determined the issue will not be swept under the carpet but, at the same time, wants to be sure there is no vendetta against the Newcastle striker, who will lead England in the World Cup Finals this summer.
The FA have dismissed reports that they have decided to charge Shearer with misconduct following his challenge on Lennon. FA spokesman Steve Double said: "It's pure speculation. The case is yet to be considered. The FA will make a decision on the case during the course of next week."
It had been reported that Shearer will appear before the FA on Tuesday and be given two weeks to answer a charge of misconduct.
Shearer has categorically denied aiming a kick at Lennon and insists it was an accident. After the incident, Shearer said: "I have now seen the television pictures of the incident and am amazed how bad it looks by comparison to what actually happened.
"I was brought down by Lennon over by the touchline and we both fell clumsily. As I tried to get to my feet I had to really tug my left foot free and the momentum of doing this looked on TV like a kick.
"It certainly wasn't. If I did accidentally catch him I certainly did not mean to. I would never deliberately hurt a fellow professional."
Shearer tried to end the controversy on Saturday - but admitted: "I won't change - and no one will change me."
He added: "I've come in for some criticism over the last few days, but all along I said it was an accident - if you don't believe me ask Neil Lennon himself, he'll tell you it was.
"I wasn't born with the skills of Best or Pele, my game is commitment. I am committed. I've been that all my life."