US Defense Secretary James Mattis, Vice President Mike Pence and Deputy Secretary of Defense Patrick Shanahan pause before entering the Pentagon, August 9, 2018, in Arlington, Virginia. (Photo: VCG)

US President Donald Trump on Sunday announced he will replace Defense Secretary James Mattis with his deputy Patrick Shanahan, speeding up the Pentagon chief's planned exit days after he quit, citing key policy differences with the US president.

Mattis, 68, had said he would leave at the end of February to allow a smooth transition for the next chief of the world's top military power, but Trump – who was reportedly upset over media coverage of the stinging resignation letter submitted by the defense secretary – moved up the timetable.

"I am pleased to announce that our very talented Deputy Secretary of Defense, Patrick Shanahan, will assume the title of Acting Secretary of Defense starting January 1, 2019," the Republican leader tweeted.

"Patrick has a long list of accomplishments while serving as Deputy, & previously Boeing. He will be great!"

Trump initially praised Mattis in a tweet announcing his departure, saying that he was retiring "with distinction" and that "during Jim's tenure, tremendous progress has been made."

But Trump changed tone two days later, writing on Twitter that he had given Mattis a "second chance" after he was "ingloriously" fired by former president Barack Obama, and appearing to take aim at a line from the Pentagon chief's resignation letter about respecting allies.

"Allies are very important – but not when they take advantage of US," Trump wrote.

The announcement that Mattis would leave the administration came just after Trump stunned Washington and allies abroad in declaring that US troops would leave Syria and significantly withdraw from Afghanistan.

Mattis and others had strongly counseled the often-impulsive president against those moves – and the decorated retired general did little to hide his disagreement with Trump.