Peter Greste, Mohamed Fahmy and Baher Mohamed were sentenced to between seven and 10 years in jail after being found guilty of aiding a “terrorist group”.
Mr Sisi was quoted by the al-Masry al-Youm newspaper late on Sunday as saying the trial had “very negative effects”.
His remarks received a mixed response from the journalists’ families.
Foreign governments, media organisations and human rights groups accused the Egyptian authorities of restricting freedom of speech.
Al-Jazeera said it defied “logic, sense and any semblance of justice”.
At a meeting with local journalists on Sunday, President Sisi sought to counter claims that the case had been politically motivated.
“The verdict issued against a number of journalists had very negative effects; and we had nothing to do with it,” he said, according to al-Masry al-Youm. “I wished they were deported immediately after they were arrested instead of being put on trial.”
Mohammed Abdul Hadi Allam, the editor of the state-run al-Ahram newspaper, and Imad Hussein, the editor of the private daily al-Shurouq, confirmed to the BBC that the quotes were accurate.
The president had wanted to distance himself from the case, insisting he would not interfere with the judiciary.
His latest remarks will therefore raise hopes that he might issue pardons to set the journalists free, but under the Egyptian law such pardons can only happen after the appeals process had ended.
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