The United States Africa Command (Africom) has begun withdrawing troops from the continent in line with the Trump administration's priorities.

The US plans to pull out about 10 percent of its 6,000 soldiers and military-affiliated civilians stationed in sub-Saharan countries in the next three years.

This was revealed by Africom commander Gen Thomas Waldhauser at a security conference in Munich on Wednesday.

Gen Waldhauser said the troops will be deployed to missions where the US sees as high-priority.

“We all realise, you know, Africa, with regards to the prioritisation of our national interests ... there’s no doubt about the fact that that it’s, you know, it’s not number one on the list," Gen Waldhauser was quoted as saying.

The Trump administration views preparation for potential conflicts with China or Russia to be of higher priority than combating terrorism in Africa.

Gen Waldhauser noted that a Pentagon review had concluded that Islamist militants in Somalia and other African countries lack the capacity to strike the US homeland.

“So it was determined that ... we as the United States could perhaps accept some risk inside the continent with regards to our forces," he was quoted as saying by the Military Times, a Washington DC-based newspaper.

The plan to reduce America's military presence is Africa was approved by the Pentagon in November last year.

The decision came on the back of a political furore that erupted following the killing of four US soldiers in October during a counter-insurgency operation in Niger.

The US Marine Corps general said the drawdowns will be done proportionally across US Special Forces and conventional fighting units in the continent. The first unit is expected to have left by June next year with the second exiting by January 2022.

The troops will be reassigned to missions elsewhere in the world.

Africom was established in 2007 to enable US military work more closely with African armies in the fight against militants.

Africom is, however, not headquartered in any African country but in Stuttgart, Germany.

Some of the countries where the US has deployed its troops are Libya, Niger, Nigeria, Cameroon and Somalia.

In Djibouti, the US set up its only permanent base in Africa whose missions mainly target terrorists in nearby Yemen.

“Is that a withdrawal from the continent?" Gen Waldhauser posed, trying to address concerns that may arise.

"Is that going to allow the Chinese and Russians to have more influence?”

“Those are the questions you have to ask and our job, I think, is ... certainly in terms of the relationship-building, is to ensure our partners, through our actions, that, you know, we are not abandoning them.”