Sixteen MPs made secret repayments in the 2008/09 financial year and it's thought that dozens more mired in the expenses scandal have agreed similar arrangements.
However, it has now emerged that Mr Lyon is taking advantage of a little-known Parliamentary rule that allows complaints about financial misconduct to be settled behind closed doors.
The deals are made available to MPs who are willing to admit they have broken the rules and offer to make voluntary repayments.
They have to privately apologise to the Committee of Standards and Privileges, the group of MPs overseeing the conduct of politicians - but their misconduct is then not made public.
It is not clear why the identities of those making repayments are not made public in the same way that criminals pleading guilty who do not face a full court trial are named...
...Last night, a spokeswoman for Mr Lyon refused to disclose how many MPs had been privately allowed to repay money or who they were. She also refused to say how many MPs were being investigated and their identities.
The Metropolitan Police are also understood to be growing frustrated by Mr Lyon’s intervention in cases involving potential fraud.
Lyon has justified using the procedure “where there was no clear evidence that the breach was intentional and it was at the less serious end of the spectrum,” but it isn't for John Lyon to decide on intent or what constitutes 'serious' in the eyes of the voter and then do secret deals. It's clear that voters must confront MPs seeking re-election and question them directly. If in doubt, kick them out.
The aftermath of the MPs' expenses fiasco has been marked by headless chickens instigating reviews and inquiries: Sir Thomas Legg; the Kelly Report; John Lyon. No wonder the Met Police claim to be 'frustrated' in their own enquiries.
Over to Brown, Clegg & Cameron who have all said that the Kelly Report should be implemented in full yet allow this rotten state of affairs to continue. Name all the MPs who have abused the system and let their constituents decide.