Both the Blues and the FA have come under fire from the Society of Black Lawyers (SBL) for their failure to report Clattenburg to the Police over allegations that he had racially abused John Obi Mikel during the Blues' defeat to Manchester United at Stamford Bridge in October.
Chelsea's complaint to the FA over the matter is currently being investigated but the SBL moved to notify police of the incident after neither party passed concerns on.
Scotland Yard has since confirmed that it cannot take any action against Clattenburg "because no victims had come forward", leading the SBL to suggest that an agreement had been struck between the football governing body and the west London club.
But Carlisle disagrees with the SBL's stance, telling reporters: "I think it would have been better if it remained within the remit of Chelsea and the FA to put any subsequent case to the Met Police.
"It is an allegation they are currently investigating themselves. If we reported all incidents from third-party evidence, there would be many investigations the police would have to go through.
"We have to have faith Chelsea have reported the incidents in good faith and that the FA will deal with it accordingly and report it to the police if necessary."
|"We have to have faith Chelsea have reported the incidents in good faith and that the FA will deal with it accordingly"
- Clarke Carlisle on Mark Clattenburg
The FA is expected to announce the outcome of its investigation into Chelsea's complaint by Saturday or Sunday and Carlisle is insistent that the matter should be dealt with effectively whatever the outcome.
"It is vital that, should Mark Clattenburg be found innocent by the FA and there is no charge for him to answer, as much as there was a furore around the allegation, there should be as much attention on his vindication," the 33-year-old added.
"It is also equally vital that if he is subsequently charged and found guilty that the correct sanctions are imposed.
"We should not be sensationalist about this. We should focus on the mechanisms that are in place so that incidents that occur are dealt with accordingly to everybody's satisfaction."