Trump's Tuesday tweet - in which he said "all reference was pointing to Qatar" as a financer of extremism - was especially surprising given Qatar's role as host of the largest U.S. airbase in the Middle East.
Qatar's Foreign Minister Sheikh Mohammed Bin Abdulrahman al-Thani told CNN that FBI investigators have confirmed that the agency was hacked and a fake article was inserted into the agency's system.
"So good to see the Saudi Arabia visit with the King and 50 countries already paying off. Perhaps this will be the beginning of the end to the horror of terrorism!"
According to USA officials briefed on the investigation, USA investigators believe Russian hackers breached Qatar's state news agency and planted a fake news report that contributed to a crisis among the US' closest Gulf allies.
A series of tweets from Mr. Trump on Tuesday appeared to show him taking credit for Qatar's isolation.
If Qatar Airways would also suspend flights to others countries, it was not immediately clear.
Trump spoke by telephone with Saudi Arabia's ruler King Salman later Tuesday in an exchange of notably different tone from the United States president's earlier remarks on Twitter. Mr Trump told King Salman that a united Gulf Cooperation Council is "critical to defeating terrorism and promoting regional stability", according to a White House readout of the conversation.
The country's Foreign Ministry stated Qatar's firm stance against violence and its rejection of criminal acts, expressing condolences to the government and people of Iran and to the families of the victims.
"It's a mixed bag with Qatar", said Republican Sen.
Since then, a team of FBI investigators have been sent to Qatar's capital city of Doha to assist the Qataris in the investigation, according to Qatari and USA officials.
A senior Emirati official insisted on Wednesday that Gulf Arab states were not seeking regime change in Doha, as tensions built in a bitter feud between Qatar and its neighbours.
Gaza's Islamic Hamas rulers, a major recipient of Qatari aid, have called Saudi Arabia's call for Qatar to cut ties with the Palestinian militant group "regrettable" and said it contradicts traditional Arab support for the Palestinian cause.
However, Jordan was taking the terror allegations into consideration and acting accordingly, he said, downgrading diplomatic ties with the beleaguered state and kicking out Al Jazeera, the Qatar-based news organization.
Qatar Airways was ordered on Tuesday to close its offices in Saudi Arabia and Bahrain, following coordinated action by four Arab nations to cut ties with Qatar.
France's President Emmanuel Macron spoke to Mr Erdogan and to the emir of Qatar in separate telephone calls, saying he was ready to back "all initiatives to encourage calm".