Law officers tried to cover up the result of a probe into court comments by Cherie Blair, it is claimed.
The National Secular Society (NSS) made a complaint after she told a devout Muslim he would not go to prison because he was a "religious person".
The remark was considered by the Lord Chancellor, Kenneth Clarke, and the Lord Chief Justice, Lord Judge.
A statement suggested she had been cleared but a private letter to the NSS said the complaint was partly upheld.
The statement by the Office for Judicial Complaints (OJC) said her actions "did not constitute judicial misconduct" and "no disciplinary action is necessary", suggesting Mrs Blair had been cleared.
But a confidential letter to the NSS said they ruled the complaint was partly upheld and "expressed some concern" about the impact of her comments.
It also said Mrs Blair, wife of former Prime Minister Tony Blair, would receive "informal advice" from a more senior judge about her comments, although it claimed this was not a "formal disciplinary sanction".
Keith Porteous Wood, who leads the NSS, accused the watchdog of a "cover-up" and making a "partial and misleading statement".
Questions were raised after Mrs Blair, who sits as Cherie Booth QC, told Shamso Miah at Inner London Crown Court he would not go to prison after breaking a man's jaw during a row over queue-jumping in a bank "based on the fact you are a religious person".
The OJC issued a media statement on 10 June as a letter to the NSS was in the post.
In it, OJC case worker Sabrina Bailey wrote: "Having taken all matters into consideration and in response to your specific complaint, the Lord Chancellor and Lord Chief Justice have expressed some concern about the impact Recorder Booth's comments may have had on the public perception of the judiciary and the sentencing process.
"All judges must, of course, be very mindful of how they express themselves when dealing with sensitive issues of equality and diversity (including religion, race and sex) so as not to create the impression that some individuals can expect more leniency than others."
An OJC spokeswoman said later: "It is always open to the Lord Chancellor and Lord Chief Justice to give informal advice to any judicial office holder when they consider it appropriate.
"Such advice is not a formal sanction and does not constitute disciplinary action and, as a matter of course, when advice is given it is not made public.
"Having looked again at the letter sent to the complainant in this matter, which openly outlined the actions taken in response to the complaint made, we agree the difference between disciplinary sanction and informal advice was not clearly explained. We will ensure this is made clear in future."
A spokeswoman for Matrix Chambers said: "Cherie Booth has no further comments to add to the statement released by the Office for Judicial Complaints."