The comments came days after General Tony Thomas, the head of US special operations confirmed that the four-year-old operation was brought to a close but denied the decision was motivated by a desire to placate Russia, which backs the Assad regime.
"The Amazon Washington Post fabricated the facts on my ending massive, dangerous, and wasteful payments to Syrian rebels fighting Assad....." Trump tweeted.
The missive appeared to be a response to an article by the newspaper published hours earlier and titled "Cooperation with Russia becomes central to Trump strategy in Syria."
The United States and Russia agreed on creating de- escalation zones in southern Syria at their first meeting at the G20 in Hamburg earlier this month.
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Former president Barack Obama approved the rebel aid program in 2013 as various insurgent groups sought external support in a general uprising against the Assad regime.
Thousands of Syrian anti-government fighters were trained and armed.
Support for the program further eroded last year after the rebels lost the areas they held in the Syrian city of Aleppo under a brutal Russian-backed government assault.
US officials said last week that some of the anti-Assad forces could be absorbed into US military-supported groups fighting Islamic State.