Shortly after the hack attack and the spread of the fake news report, the UAE announced that it was banning Emiratis from accessing Al Jazeera's website.
"Al-Arabiya also reported that al-Thani said "there is no wisdom in harboring hostility towards Iran,", and that relations with the USA under the Trump administration were tense.
Qatar is set to track down and prosecute the perpetrators, officials said in a statement.
The falling out is especially awkward for the Gulf Arab states after their leaders met Trump last weekend at a Riyadh summit of Muslim nations meant to showcase solidarity against Sunni armed militant groups and Shi'ite regional adversary Iran.More news: "First Alert Weather Day" in effect: Heavy rain and strong storms possible
In the early hours of Wednesday, Qatari authorities denied the veracity of these statements, claiming that the Qatari news website was hacked.
The report published on Wednesday also said Sheikh Tamim spoke favorably about the Lebanese organization Hezbollah and the Palestinian group Hamas, while criticizing US President Donald Trump and saying he may not serve a full term.
Saudi Arabia's Okaz newspaper accused Qatar of "breaking ranks" and choosing to "side with the enemies of the nation", while the website of the Doha-based Al Jazeera network was blocked in the United Arab Emirates.
Saudi-owned Al Arabiya television ran a story titled "Proof that Qatar News Agency was not hacked", which noted that the statement had also run on Qatari state television and the QNA Instagram account. Egypt, the UAE and Bahrain should reconsider their antagonistic stance against Qatar. Regulators and government officials in the UAE did not immediately respond to requests for comment.More news: Trump's budget director Mick Mulvaney holds briefing
On Tuesday, the Qatar News Agency (QNA) quoted Sheikh Tamim Al Thani as telling a military ceremony that Iran was an "Islamic power that can not be ignored".
This year's valedictorian, Ghada Khalifa al-Thani, gave an emotional speech, saying: "One individual can not make a permanent change or development", she said."It requires the whole community to work together to achieve this".
Sheikh Saif Bin Ahmed Al-Thani, Director of the Government Communications Office confirmed that an investigation will be put in place to look into this matter. He said Qatar "will hold all those committed accountable". In 2012, a damaging virus crippled computer systems at Qatari natural gas producer RasGas soon after a similar attack on Saudi Arabia's state-run oil company.
Qatar has been at odds with Gulf states for sometime over the extent of its support for the Muslim Brotherhood, an issue that has been brought into sharper relief by Trump's demand for Gulf states to do more to fight extremism.More news: Greece looks for debt help after backing further cuts