Qatar has denied the allegations, in the biggest diplomatic crisis to have hit the region in years.
"His [Trump's] message was that we need unity in the region to fight extremist ideology and terrorist financing", a USA official told Reuters news agency.
Trump on Tuesday took credit for the Middle Eastern countries breaking diplomatic relations with Qatar.
Separately, the Pentagon thanked Qatar for hosting the largest USA air force base in the Middle East.
In a twitter message Trump has termed the Arab States decision as their support for terrorism. "It has to choose whether it must move in one direction or another direction", the minister said.
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He suggested Qatar was funding extremism.
To help Qatar clarify the issue and return to normal diplomacy, Washington sent a team of FBI investigators to Doha to probe the hacking allegations.
Al Qassemi, of the ruling family of the sheikhdom of Sharjah in the United Arab Emirates, told The Associated Press on Wednesday that he hopes Qatar ends its "rogue, maverick" ways.
In announcing it was cutting ties, Riyadh accused Doha of harboring "terrorist and sectarian groups that aim to destabilise the region including the Muslim Brotherhood, Daesh (IS) and Al-Qaeda". Some countries designate both as terrorist groups.
The BBC's Barbara Plett Usher in Washington said Qatar, Saudi Arabia and Kuwait have all funded extremists in Syria but pulled back under U.S. pressure, while Qatar, which likes to see itself as a neutral player and potential intermediary, has dealings that are arguably murkier than the others'.
Qatari Foreign Minister Sheikh Mohammed Bin Abdulrahman al-Thani told Al Jazeera that his country would not retaliate but was unhappy with regional rivals "trying to impose their will on Qatar or intervene in its internal affairs".
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The International Air Transport Association called on the countries that acted against Qatar to restore air links with the country, warning of major travel disruptions.
Disruption to airspace in the Gulf began on Tuesday morning local time.
Qatar is also a major regional diplomatic player and worldwide investor and is set to host the World Cup, football's biggest tournament, in 2022.
The UAE General Civil Aviation Authority (GCAA) is yet to revoke licences given to Qatar Airways similar to the step taken by its Saudi counterpart.
Qatar is heavily dependent on food imports and residents have been queuing at supermarkets to stockpile.
The ransom, which Iraqi officials said was in the "hundreds of millions of dollars", was believed to have been paid to militias with close ties to Tehran.
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Since the start of the crisis, non-Qatari Gulf shareholders - who often make up between 5 and 10 percent of the market's turnover - and foreigners have have been exiting positions faster than usual, according to Qatar bourse data.
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