Qatar has blamed hackers for a story on its state news agency website that quoted the emir as criticising US "hostility" towards Iran.
On Tuesday, the Qatar News Agency (QNA) quoted Sheikh Tamim Al Thani as telling a military ceremony that Iran was an "Islamic power that cannot be ignored".
The government said the agency had been hacked by an "unknown entity" and that the story had "no basis whatsoever".
However, the quotes were reported across the region and caused a stir.
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.
Ties between Qatar and its Gulf Arab neighbours have been strained in recent years by the emirate's support of Islamist groups, including the Muslim Brotherhood, and its funding of Al Jazeera, which they see as being overly critical.
The report on the QNA's website said Sheikh Tamim had told the military ceremony that Qatar had "tensions" with the administration of US President Donald Trump, who on Sunday urged Arab and Muslim leaders to "work together to isolate Iran".
The emir was quoted as saying that there was "no wisdom in harbouring hostility toward Iran" and that it was a "big power in the stabilisation of the region".
He was also reported to have described relations with Israel as "good" and called Hamas the "legitimate representative of the Palestinian people".
State television's nightly news bulletin showed pictures of the ceremony and included lines from the QNA report in the ticker at the bottom of the screen.
On Wednesday, Government Communications Office director said the QNA website "has been hacked by an unknown entity" and "a false statement attributed to His Highness the Emir Sheikh Tamim bin Hamad Al Thani has been published".
"The statement published has no basis whatsoever, and the competent authorities in the State of Qatar will hold all those [involved] accountable."
Qatar's foreign ministry meanwhile denied that its ambassadors to Saudi Arabia, Egypt, Kuwait, Bahrain and the UAE were being withdrawn.
A series of posts on the QNA's Twitter feed cited Foreign Minister Mohammed bin Abdul Rahman Al Thani as saying a plot to "discredit" the country had been uncovered. The ministry said the remarks were "fabricated" by hackers.