"During my recent trip to the Middle East I stated that there can no longer be funding of Radical Ideology. Leaders pointed to Qatar - look," he tweeted Tuesday.
The tweet could pose difficulties for the US in explaining why it remains in Qatar, host to the one of the Pentagon's largest military bases in the Middle East and a linchpin in the campaign against ISIS. For that reason, the President's 140 character blast may raise concerns within the Defense Department.
Pentagon officials moved quickly to limit any damage, with spokesman Capt. Jeff Davis telling reporters Tuesday that the US is "grateful to the Qataris for the longstanding support for our presence and their enduring commitment to regional security."
He added that the US has "no plans to change our posture in Qatar," stressed that there has been no impact on military operations and urged all parties to work together to resolve the crisis.
Defense Secretary James Mattis called his Qatari counterpart Tuesday to discuss the situation, a US defense official said. There was no formal readout on the call, but a second defense official said it was an effort to keep the dialogue open on positive military relations between the two countries.
State Department spokeswoman Heather Nauert said the US was informed of the Gulf nation's decision, but only "immediately prior" to the announcement being made.
Nauert said Qatar has made some progress on reducing terror financing, "however, let me make this clear," she added: "They have made progress, but they still have work to do, more work needs to be done."
And like Davis, Nauert struck a different note than Trump did, saying that the US is "grateful to the Qataris for their longstanding support for our presence in the region."
Amid the mixed messaging, White House press secretary Sean Spicer declined to say whether Trump encouraged Saudi Arabia and other Arab countries to cut ties with Qatar after Trump appeared to claim credit for the move on Twitter.
Spicer said the US "wants to see this issue deescalated and resolved immediately" and said regional cooperation is "so important."
Analysts say Trump's Twitter intervention calls into question the role of the US as an impartial arbiter in the region.
"The President has just sided with everyone else rather decisively," said Hussein Ibish, a senior resident fellow at the Arab Gulf States Institute. "The administration's two priorities are confronting terrorism and Iran, that's exactly what this is about," Ibish said. "The chance of the US siding with Qatar, giving them a face-saving way out, is totally gone."
The President did not express concern or condemn the move by Saudi Arabia, Bahrain, Egypt and the United Arab Emirates to break off relations with Qatar in the worst diplomatic crisis to hit Gulf Arab states in decades.
Instead, he offered praise, tweeting Tuesday morning that it was "so good to see the Saudi Arabia visit with the King and 50 countries already paying off. They said they would take a hard line on funding extremism, and all reference was pointing to Qatar. Perhaps this will be the beginning of the end to the horror of terrorism!"
The tweets were a 180-degree reversal of his own position on Qatar, a nation he commended during a May 21 summit in Saudi Arabia, saying relations were "extremely good."
"He highlighted the relationship between the US and Qatar as a strategic one and noted that Qatar hosts a major airbase and today he characterizes it a financier of radical ideology," said Eric Trager a fellow at the Washington Institute for Near East Policy. "The question is why? Why the change?"
The shift could create difficulties for the Pentagon. Trager notes that Qatar is a country in which American interests and values are "in great tension."
"The Pentagon sees Qatar first and foremost as the country hosting a major airbase and President Trump appears to have, in light of this crisis, focused more on what Qatar is promoting ideologically over what Qatar is providing for American forces. That's the basic trade-off here."
The three Sunni Gulf countries and Egypt accused Qatar of supporting terrorism and destabilizing the region, in part because of its ties to their Shiite rival, Iran. Yemen, Libya and the Maldives also cut ties with Qatar.
The squabble could disrupt the US-led campaign against ISIS, particularly since the main regional center for daily air missions and coordination of air operations is the US military's Al Udeid Air Base in Qatar.
The Persian Gulf nation of 300,000 people is now the subject of a blockade by some of its closest neighbors. They have closed down air and sea links with Qatar and have said they will look for ways to block other nations from flying through their airspace on the way to Qatar.
The crisis could ripple globally. Qatar is the world's top exporter of liquefied natural gas and a crucial energy supplier to Europe and Asia.
Saudi Arabia has also shut the local office of the Qatar media group Al Jazeera.
Qatar -- which shares its only land border with Saudi Arabia -- has rejected the accusations, calling them "unjustified" and "baseless."
Sheikh Mohammed bin Abdulrahman Al Thani, speaking to CNN's Becky Anderson Tuesday, said a Saudi Arabian statement accusing his country of terrorism was "full of false information."
"With all due respect, this statement is full of contradictions because it is saying that we are supporting Iran and on the other hand supporting the extremist groups in Syria; and we are supporting the Muslim Brotherhood in Saudi or in Yemen and we are supporting the (Iranian-backed) Houthis form the other side. In all battlefields, there are adversaries," Al Thani said.
Qatar's independent Emirs have long pursued their own foreign policy path, to the irritation of Saudi Arabia. And while Doha admits to supporting Islamic movements such as the Muslim Brotherhood and Hamas, it denies any support for terrorism.
"Is the government of Qatar financing terrorists? The evidence of that is very tenuous," Trager said. "But is Qatar, through its media outlets, promoting a certain type of ideology? Yeah."
It wasn't clear if the President had discussed his tweet with either the State or Defense departments beforehand, and queries to the White House were not immediately returned. But he struck a very different note than his Cabinet officials.
Asked about the Gulf blockade at a Monday press conference in Australia, Defense Secretary James Mattis said, "I am positive there will be no implications coming out of this dramatic situation at all and I say that based on the commitment that each of these nations ... have made to this fight."
Secretary of State Rex Tillerson, speaking alongside Mattis, also downplayed the possibility of negative repercussions for the fight against terrorism and urged the parties to stay unified. "We certainly would encourage the parties to sit down together and address these differences," he said.
Qatari citizens have been told they have 14 days to leave Saudi Arabia, Bahrain and the UAE, and those countries also banned their own citizens from entering Qatar.