The party has called in the Electoral Commission to investigate after a gift was apparently accepted from the 'stepfather' of a journalist posing as a businessman.
Lib Dem peer Lord Strasburger, who is said to have been caught on camera discussing how to circumvent disclosure rules, has resigned the party whip while the probe takes place.
Clegg was reportedly filmed by Channel 4's Dispatches meeting the fake businessman.
The allegations follow another sting by the Daily Telegraph earlier this month, in which a reporter was told they could give money through a cousin and met Chief Secretary to the Treasury Danny Alexander.
A Lib Dem spokesman said: "It is common practice for senior party figures from all parties to meet with potential and current donors.
"Dispatches has raised important questions about one particular donation, which the party is taking seriously. The Party had no reason to believe that the donation was made by anyone other than the person who signed the cheque.
"When we were alerted to the claim that this donation may, without our knowledge, have been made on someone else's behalf, we referred this matter to the Electoral Commission, and requested their advice on whether the donation should be handed to the Commission or returned to the donor. We shall comply fully with their investigation and any recommendations they may make as a result
"The party has also introduced an additional level of scrutiny to donations to the federal party, over and above legal requirements. This will apply with immediate effect.
"Lord Strasburger denies any allegation of wrongdoing. He has referred himself for investigation by the Electoral Commission and has also decided to resign the Liberal Democrat Whip in the House of Lords while that investigation is underway."
Lord Strasburger said: "I have been told about a programme planned to be broadcast on Channel 4 Dispatches on Monday which will include details of a donation made to the Liberal Democrats in which I was involved.
"In the last few months I have been very active in the House of Lords fighting to protect the freedom of the press, but I never had in mind the sort of cynical and contrived entrapment-style journalism to which I have been personally subjected by Channel 4.
"I am a retired businessman, I am not a career politician ... In a purely voluntary capacity, I have been helping the party with fundraising. I have gained no personal benefit in doing so.
"Whatever Channel 4 may say in their Dispatches programme, I do not think I have committed any offence. Having said that, I believe that we should all be accountable for what we do, so I have invited the Electoral Commission to carry out an investigation into my actions.
"In the meantime, whilst I maintain that I have committed no offence, I have stopped fund-raising for the party. Also, for the sake of the party, I have resigned the Whip from the Liberal Democrat group in the House of Lords until the investigation is completed."