In addition to Morsi's conviction being upheld and receiving a life sentence, two journalists from the Qatar-based state-funded broadcaster Al-Jazeera were also handed death sentences.
But in a statement released late yesterday by Qatar's foreign ministry, officials in Doha said the verdict was unfounded.
"Though it is not final, the verdict is unfounded, goes against truth and contains misleading claims which are contrary to the policy of the State of Qatar towards all sister countries, including Egypt," said the ministry's director of information, Ahmed Al Rumaihi.
Rumaihi added that the verdicts lacked "the proper sense of justice".
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Morsi, who has been sentenced to death in a separate trial, was Egypt's first democratically elected president but the army overthrew him in 2013.
He was given life in prison yesterday for leading an unlawful organisation and 15 years for having "stolen secret documents concerning state security," his lawyer said.
But Morsi was acquitted of having supplied classified documents to Qatar, one of his main backers, Abdel Moneim Abdel Maksoud told AFP.
In a separate statement yesterday, the media network denounced the verdict as an attack on the free press.
Egypt has long accused Qatar -- and Al-Jazeera -- of being sympathetic to the Muslim Brotherhood.