The WRU won the backing of the clubs in two votes based on resolutions put before the meeting in the Princess of Wales Theatre, Port Talbot.
The size of the majority votes strengthens the mandate of the WRU Board and Executive to manage the game in Wales.
The first resolution to be voted on by delegates cited that the Board had not been acting in the best interests of Welsh rugby while the second had called for a vote of no confidence in the current Board.
The first resolution failed to pass when 94% of the delegates voted by 453 votes in favour of the Welsh Rugby Union. There were only 18 against (4%) and 13 abstentions (3%).
The WRU won the confidence of the delegates by 95% when 462 voted for the governing body with four against (just 1%) and 18 abstentions (4%).
The meeting which was attended by a record number of delegates, was chaired by WRU President, Dennis Gethin.
At the meeting the WRU chairman agreed to ask the Board to sanction a ballot on whether the proposed new national league structure of the amateur game will go ahead or whether the existing structure will be retained for next season.
WRU Chairman, David Pickering, said after the meeting: “Today there has been an overwhelming vote of confidence in the Welsh Rugby Union.
“The clubs of Welsh rugby have exercised their constitutional right to question the governing body and we have taken part in a full and frank debate.
“The ability to call an Extraordinary General Meeting is enshrined in our corporate articles of association as a forum for clubs to raise issues between the Annual General Meetings.
“The Welsh Rugby Union has to listen to its member clubs and we are determined to focus on ensuring a meaningful dialogue takes place on all important issues.
“Welsh rugby is continuing to evolve and now we must work together to make sure we build on our successes of the past and face up to our challenges of the future.”
The Group Chief Executive of the WRU, Roger Lewis, added: “We are delighted that the clubs of Welsh rugby have been able to take part in a full and open debate.
“The incredible support shown for the WRU gives us the confidence to go forward with energy and focus to continue to evolve the game in Wales.
“The discussion in the meeting covered a range of issues and we will ensure that we will engage fully with our clubs to find the right solutions.
“The men and women of Welsh rugby have spoken and their voices have been heard. We now want to focus on the business of running Welsh rugby as both the professional and amateur levels of the game continue to evolve.
“We have all learnt lessons from this debate and we will ensure the dialogue we have engaged in today continues to help us develop and improve.”
