"A false statement attributed to His Highness has been published", the Gulf Arab state's government communications office said.
The allegedly fake report on the website of Qatar News Agency (QNA) cited Sheikh Tamim bin Hamad al-Thani, Qatar's emir, as criticizing the latest increase in tension between Saudi Arabia and Iran, in a speech he gave to graduating military cadets.
They included calling Hamas "the legitimate representative of the Palestinian people", as well as saying Qatar had "strong relations" with Iran.
"The state of Qatar has been surprised by the actions of certain media outlets and satellite channels", the Foreign Ministry said in a Wednesday statement.
The "false statement" was reported by broadcasters in the United Arab Emirates and caused a stir on social media in the Gulf, before Doha scrambled to deny the claims.
Al-Jazeera English's website was briefly inaccessible, though internet users could reach it later Wednesday morning.
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In an embarrassing incident that has the Qatari government bending over backward to fix its "tarnished" reputation in the face of its petrodollar-fueled and USA -backed Gulf allies, the state-run Qatar News Agency took down an article that defended all of Hezbollah, Hamas and Iran, claiming the site was hacked. The emir also reportedly called Iran an "Islamic power" and said Qatar's relations with Israel were "good".
The incident happened days after Qatar complained it was the target of "an orchestrated barrage" of criticism by unknown parties in the run-up to Trump's visit alleging the Gulf state supported militant groups in the Middle East. In a tweet, the QNA said "the state of Qatar will investigate this matter" and hold all involved accountable. It declined to immediately comment further.
Arguments over the Brotherhood, the most influential Islamist group in the world, were at the heart of a rift among Gulf Arab states that in 2014 saw Saudi Arabia, the UAE and Bahrain withdraw their ambassadors from Doha. Eight months later, they returned their ambassadors as Qatar forced some Brotherhood members to leave the country and quieted others. Western officials also have accused Qatar of allowing or even encouraging funding of Sunni extremists like al-Qaida's branch in Syria, once known as the Nusra Front.
Qatar is also home to the former Hamas political bureau chief, Khaled Meshaal, who has lived there in exile for several years.
There were also alleged negative remarks about Qatar's relationship with the new administration of US President Donald Trump.
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