Clarke complained about the incident after the Aberavon meeting, saying he had been insulted.
But although the WRU panel - advised by president Dennis Gethin - agreed, they decided Lewis' apology to Clarke after the AGM was sufficient.
A statement of behalf of WRU president, Gethin, stated: "The Welsh Rugby Union has reviewed the contents of an email it received from the chairman of the Premiership division clubs and secretary of Cross Keys RFC, Chris Clarke, involving the Group Chief Executive of the WRU, Roger Lewis.
"It follows a verbal exchange which took place at the end of the recent WRU Annual General Meeting in Aberavon as the hall was clearing and some delegates were discussing the vote on reform of the Premiership Division.
"The President of the WRU, Dennis Gethin, looked into the points raised and has spoken to eight individuals who were present, including Mr Clarke and Mr Lewis.
"He has concluded that comments made by the secretary of the Cross Keys Rugby Football Club were regarded by Mr Lewis as a direct, personal insult and an insult to the Board of the WRU.
"Mr Lewis reacted to the comments in a heated exchange with Mr Clarke.
"Mr Lewis then attended a press conference but returned minutes later and apologised to Mr Clarke for his part in their conversation.
"The panel, advised by the President, has noted the apology and found, on behalf of the WRU, that this concludes the matter and no further action is necessary."
WRU chairman David Pickering, WRU Vice Chairman Ken Hewitt and WRU board member Martin Davies made up the panel.