President Trump has publicly expressed his support for the move of Gulf nations to cut Diplomatic Ties with Qatar, a key U.S. ally, as opposed to Pentagon and State Department’s opinion to stay neutral.

Trump, in a tweet Tuesday stated that during his trip to the Middle East, he pioneered a motion to stop funding radical ideology and other leaders felt he was referring to Qatar.

Questions have been raised on how to reconcile U.S. military activities in Qatar with President Trump’s tweet.

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Qatar plays host to one of United States largest military bases [VIDEO] in the Middles East. Trump’s pronouncement may cause unrest within the Defense Department.

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Jeff Davis, Pentagon’s spokesperson in a bid to limit the damage, said that the U.S. was thankful to Qatar for hosting them for this length of time and for their role in promoting peace in the region.

He also said that the U.S. was happy with the relationship, emphasized that its military operations were geared in the right direction and urged all parties to work in unity to end the crisis.

Heather Nauert, spokeswoman for State Department said the U.S. was only told just before the announcement of the decision taken by the Gulf nations.

Nauert commended Qatar for its efforts in reducing terror sponsorship and encouraged them to put in more efforts to resolve the issue permanently.

Trump tweet may imply U.S. partisanship

Nuaert also thanked Qataris for their hospitality and for hosting the U.S. military.

Within the conflicting statements, White House press secretary Sean Spicer refused to say whether Trump influenced the decision of the Arab countries to cut ties with Qatar because the president’s tweet implied such.

Spicer reiterated that the U.S.’s desire was for the issue to be resolved amicably and for all the parties involved to work together as a team.

According to analysts, Donald Trump’s tweet may imply U.S. partisanship in the region. Hussein Ibish, a fellow at the Arab Gulf States Institutes said the President was on the side of everyone except Qatar.

The president’s tweets were contradictory to his stands on Qatar, a country he praised during a summit in Saudi Arabia, saying cooperation was important.

Eric Trager, a fellow at the Washington Institute, said the ties between Qatar and the U.S. was critical and recounted that the U.S. had an airbase in the same nation Donald Trump described as a sponsor of radical ideology.