This is a change from the policies of the previous Obama Administration under which the Department of Defence was authorised to carry out such strikes and the CIA used drones to gather intelligence information, The Wall Street Journal reported, citing unnamed sources.
The White House and the CIA have so far not responded to the news report.
According to the daily, Trump gave such an authorisation to the CIA not long after he visited its headquarters on January 21.
The report said Trump's unexpected decision to give the CIA the strike authority created ferment inside the US government within days of his visit, as US military officials scrambled to respond to the new directive.
According to New America's research -- a Washington DC based think-tank -- before Obama changed his policy and only authorised the Department of Defence to carry out drone strikes, CIA's drone strikes were mostly used in Pakistan.
US drone strikes were halted in the last eight months of the Obama Administration.
In recent weeks, top Pentagon generals have expressed concerns over the continued presence of terrorist safe havens in Pakistan.
CIA drone strikes were quite successful in elimination of high profile terrorists from the safe havens of Pakistan.
"The United States has killed more than 50 al-Qaeda and Taliban leaders in Pakistan since the beginning of the CIA drone campaign," Bergen and Sterman wrote in the CNN op-ed.
"Under Obama, the drone war in Pakistan reached its height, and Trump, should he choose to do so, can easily bring that war back," the two American scholars said and had predicted that Trump may well escalate the drone war in Pakistan and there is not much to stop him if he chooses to do so.
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