In an article for the Huffington Post, Clooney said it was "experts in Egyptian affairs" who issued the warning over a February 2014 report for the International Bar Association, not the authorities, as was reported in The Guardian.
The Guardian has not changed its story, however, which was based on an interview with Clooney last week following an appeal hearing for one of her clients, one of three Al-Jazeera journalists detained in Cairo.
Clooney, a leading barrister who married Hollywood actor George Clooney last year, is on the defence team for Egyptian-Canadian journalist Mohamed Fahmy.
The Huffington Post article, written with her co-counsel Mark Wassouf, said the warning delivered over the IBA report was "entirely unrelated" to the Al-Jazeera case.
"This incident arose before Mrs Clooney's involvement in the Fahmy case, before the current (Egyptian) president was in office and in a context entirely unrelated to this case," they wrote.
The Guardian story reported how Clooney helped compile a report that raised questions about the independence of judges and prosecutors in Egypt.
"When I went to launch the report, first of all they stopped us from doing it in Cairo," she was quoted as telling the newspaper.
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"They said: 'Does the report criticise the army, the judiciary, or the government?' We said: 'Well, yes.' They said: 'Well then, you're risking arrest.'"
The newspaper said the warnings were from the Egyptian authorities, but interior ministry spokesman Hani Abdel Latif had challenged this assertion.
"We have nothing against her," Latif told AFP this week.
Egypt's top court last week ordered a retrial of Fahmy and the other Al-Jazeera journalists, Australian Peter Greste and Egyptian Baher Mohamed.
But Fahmy's defence team are hoping to get their client deported.
"The focus today should not be on the risks that lawyers or journalists faced in the past. The focus should be on the risks of free speech in today's Egypt," Clooney and Wassouf wrote.
"We consider it a promising sign that President Sisi has stated that he would consider pardoning Mr Fahmy. It would be a promising sign if the authorities agreed to transfer him to Canada."