Thompson addressed all BBC staff in an in-house broadcast today, telling them the corporation needed to put its house in order after "unacceptable behaviour" from production staff.
He is introducing a mandatory training programme for all 16,500 programme and content staff, called "safeguarding trust", from the autumn.
The address followed his four hour meeting this morning with the BBC Trust, which has said it is deeply concerned and not ready to draw a line under the affair.
It has told Thompson to stiffen discipline and that it may take additional measures when it receives his final report on the breaches in the autumn. It will also start to track public opinion on whether the BBC is trusted.
The 'A Year with The Queen' affair is prominent in the Trust's concerns, and its chairman is today writing to Buckingham Palace to apologise on the Trust's behalf for the events around the promotion of the documentary.
However, six other editorial standards breaches have been turned up by the BBC's internal investigation into programming since January 2005.
The breaches, mostly relating to production staff posing as competition entrants, were committed on programmes including Comic Relief 2007 and Sport Relief 2006, while BBC Radio was also criticised for poorly organised competitions.
It is not clear which staff members have been or are at risk of being suspended, but the BBC statement said: "In some cases, editorial leaders will be asked to stand back from their duties, pending reviews of why it took so long for a number of historical incidents to come to light."
A BBC spokeswoman said that Peter Fincham's position was safe; the controller of BBC One played a key role in breaking the erroneous story that the forthcoming 'A Year with The Queen' documentary showed the Queen walking out on photographer Annie Leibovitz.
RDF has taken the blame for handing the BBC a preview tape which reordered the footage to give this false impression. However, the BBC is mounting an investigation into how its staff failed to check the facts. The inquiry report will be made public.
Last week, Ofcom fined the BBC £50,000 for the incident in which a member of the 'Blue Peter' production team posed as a viewer when a competition entrant could not be found.
For further details of competition breaches please click here.