Among the issues allegedly addressed by the Qatari ruler were the Palestinian-Israeli conflict, strategic relations with Iran, and comments about Hamas.
There were also alleged negative comments about Qatar's relationship with the new administration of US President Donald Trump.
Doha though said the statement was completely untrue.
"The Qatar News Agency website has been hacked by an unknown entity," reported the Government Communications Office in a statement.
"A false statement attributed to His Highness has been published."
It added that an investigation would be launched into the security breach.
At this stage it was unclear who was behind the hack.
The "false statement" said the emir spoke on Tuesday, two days after the Qatari leader and Trump met in Saudi Arabia as part of the president's recent visit to the Middle East.
The remarks posted on QNA as a result of the hack were picked up and reported by broadcasters in the region, including some in the United Arab Emirates.
They also caused a stir on social media in the Gulf, before Doha scrambled in the early hours of Wednesday morning to deny the claims.
The communications office added that the "State of Qatar will hold all those" who committed the breach accountable.
Qatar is home to the former leader of Hamas, Khaled Meshaal, who earlier this month used his Doha base, where he has lived in exile for several years, to launch a new policy document.
Last weekend, Doha said it had been the victim of an orchestrated smear campaign over its alleged "support" for terrorism.
(This story has not been edited by NDTV staff and is auto-generated from a syndicated feed.)