The Football Association has launched an urgent review into "deficiencies" that led to the debate on coach Sven-Goran Eriksson's future.
Eriksson kept his job because he had "no case to answer" after his affair with secretary Faria Alam.
But chief executive Mark Palios resigned and communications director Colin Gibson also quit.
The FA said on www.theFA.com: "Deficiencies surrounding management procedures have been exposed."
English football's governing body will conduct a full investigation into the circumstances surrounding recent events.
It has been left to confront the fact that, while chairman
Geoff Thompson and executive director David Davies were not publicly censured, there had been serious management failings over the past month.
While Eriksson was cleared of the main charge of lying to his bosses, being deemed to have "no case to answer", the board was left to wrestle with the question of how a false statement denying an affair with Alam was ever
put out at all.
Just a few days later it had to be contradicted, sparking the investigation which led to Thursday's emergency board meeting.
Indeed, both Thompson and Davies are likely to have been left in no doubt by their colleagues that there had been failings on their part.
As the FA now searches for a new chief executive, two senior figures - Premier League chairman Dave Richards and Roger Burden, from the amateur side of the
game with experience of running the Cheltenham & Gloucester Building Society - have been asked to "support" Thompson.
A statement on the FA's website, www.theFA.com, revealed: "This entire episode has been regrettable for the reputation of football in this country but
the board remain determined to restore the highest standards.
"Deficiencies surrounding management procedures have been exposed and the board is collectively resolved to see these corrected.
"An immediate review will be instituted with appropriate consultation," the statement added.