The Deputy Prime Minister said his office had heard of "indirect and non-specific" claims about Lord Rennard's conduct in 2008, and "acted to deal with them".
"My Chief of Staff at the time, Danny Alexander, put these concerns to Chris Rennard and warned him that any such behaviour was wholly unacceptable," Mr Clegg said in a statement.
"Chris Rennard categorically denied that he had behaved inappropriately and he continues to do so. He subsequently resigned as Chief Executive on health grounds.
"As my office only received concerns indirectly and anonymously, as those involved understandably wanted to maintain their privacy, there was a limit to how we could take this matter forward following Chris Rennard's resignation."
In full: Nick Clegg's statement about Lord Rennard's behaviour
Lord Rennard - a key party strategist and adviser to a succession of Lib Dem leaders before standing down due to ill health in 2009 - has said he is "deeply shocked" by the allegations, which he "strongly disputes" and regards as a "total distortion" of his character.
The Liberal Democrat leader said the allegations made on Channel 4 News last Thursday had been "extremely serious and distressing to the women involved".
"It is critical they are investigated thoroughly and dealt with properly and they will be," he insisted.
"But I would like to make one thing crystal clear. I did not know about these allegations until Channel 4 informed the party of them shortly before they were broadcast.
"I have today spoken to one of the women in the broadcast whom I respect and admire and who confirmed that she had never raised the issue with me.
"I am angry and outraged at the suggestion that I would not have acted if these allegations had been put to me.
"Indeed, when indirect and non-specific concerns about Chris Rennard's conduct reached my office in 2008, we acted to deal with them."
Mr Clegg said there were "legitimate concerns that issues raised with the party were not handled as well as they should have been".
He said an independently chaired review would be held into Lib Dem procedures and how they were applied at the time.
A separate investigation will be carried out into Lord Rennard under the party's disciplinary process.
"I am absolutely determined that both these investigations will be carried out thoroughly and comprehensively," he went on.
"These investigations may well reveal flawed procedures, and clearly the women concerned feel they were not properly listened to. But I totally reject the insidious suggestion that my office or I are responsible in any way for a deliberate cover-up.
"The full truth of what happened and what failed to happen and who said what to whom will be revealed by these investigations.
"But in the meantime, I will not stand by and allow my party to be subject to a show trial of innuendo, half-truths and slurs.
"The important thing is that we respect the women who have come forward and do everything to get to the truth. That is what will now happen.
The statement came after several days in which the Lib Dems insisted Mr Clegg had not been aware of allegations about Lord Rennard until the Channel 4 broadcast last week.
Two Lib Dem ministers, Vince Cable and Jeremy Browne, took to the airwaves this morning repeating the denials on behalf of the leader - who has been on a family holiday in Spain.
Asked whether he had previously been aware of complaints against the peer, Business Secretary Mr Cable said: "Absolutely not... Nick Clegg has also said he was not aware of these allegations until they appeared on TV last week."
However, doubts were fuelled when the Mail on Sunday reported that one of the women who complained suggested Mr Clegg knew in a Facebook discussion in January 2009.
The newspaper suggested that several years ago Mr Clegg's political adviser Matthew Hanney had asked one of the alleged victims: "Do you mind if I speak to Nick about it?"
The Daily Telegraph also said they put allegations about Lord Rennard to Mr Clegg's chief of staff Jonny Oates nearly three years ago.
The Channel 4 News report featured several women had claimed Lord Rennard touched them inappropriately.
One of them, Alison Smith, a Lib Dem activist who is now a lecturer at Oxford University, said she had spoken to both the then Lib Dem chief whip Paul Burstow and the party's spokeswoman for women and equality, Jo Swinson, about her claims, but said no action was taken.
In a statement on the Lib Dem Voice website yesterday, Ms Swinson - now equalities minister - confirmed she had looked into the issues.
"All the time I was careful to respect their wish for privacy and, for that matter, their right not to be harassed by the press," she wrote.
"I took action and ensured that others took action. I told the women who had confided in me what I had done to try to put a stop to any inappropriate behaviour, and encouraged them to let me know if they became aware of any further incidents."
Responding to the initial Channel 4 News allegations, a spokesman for Lord Rennard said: "He regards the report as a total distortion of his character.
"Not a single complaint of misconduct was made against him to his knowledge during the 27 years he worked for the Liberal Democrat party. Despite the claim made by one woman in the report, Lord Rennard continued working closely with her for ten years after the alleged event described.
"Until this matter is resolved he will withdraw from the Federal Policy Committee on which he serves and temporarily stand aside from the Liberal Democrat group in the House of Lords to seek to avoid any embarrassment to the party.
"He will remain a member of the Liberal Democrats and will continue to devote himself to good causes through his work in the House of Lords and elsewhere."
After the follow-up report on Friday, Lord Rennard said in a statement: "I am disappointed and angry that anonymous accusations from several years ago are once again being made public in this manner in a clear attempt to damage my reputation.
"Let me reiterate that in 27 years working for the Liberal Democrat party, not a single personal complaint was ever made against me to my knowledge."
Speaking on Pienaar's Politics on BBC Radio 5 Live this evening, Mr Cable said: "I knew nothing about either the general or the specific and I suspect most of my senior colleagues didn't either.
"I have got a serious job in government. There is no reason why I should have ever been involved in this at all."
He added: "I normally pick up rumours when they go around but certainly didn't hear any in his case."
Labour waded into the row - which comes with just days to go before the crucial Eastleigh by-election - to demand a fully independent inquiry be held.
Shadow equalities minister Kate Green said: "Nick Clegg's statement raises more questions than it answers about his judgment and the willingness of the Liberal Democrats as a party to properly investigate such serious allegations at the time they were made.
"At issue is not just a series of serious allegations from a number of women, but how the Liberal Democrat Party responded to those allegations.
"Only with a fully independent investigation can the public have confidence that the truth will prevail and lessons learned for the future."
