"The Afghans have to decide what Afghanistan looks like". He said he had so far not received any direction to reduce the almost 14,000 US troops in Afghanistan, but noted what he called strong USA security interests in the region.
Shanahan said a withdrawal of about half the USA troops in Afghanistan was not something that was being discussed at this point and he had not been directed to reduce troop numbers.
"It is important that the Afghan government is involved in discussions regarding Afghanistan", Shanahan said.
Thus far, the Taliban have refused to negotiate with the government of President Ashraf Ghani, calling it illegitimate.
The insurgent group claimed last week that the Trump administration had agreed to pull half of the US forces in Afghanistan out of the country in just a couple months.
"We are in the early stage of a protracted process", he said.
The U.S. denies that any timeline for a withdrawal has been agreed yet with the Taliban, though CBS News senior national security correspondent David Martin reported just before Christmas that the Pentagon had been ordered to start planning the withdrawal of roughly 7,000 troops.
Shanahan said from his plane that he had no orders to "step down our forces in Afghanistan", but was tasked with supporting ongoing peace talks between Washington and the Taliban. Those include the involvement of the Afghan government, which the Taliban refuses to acknowledge.
The US is expected to commence a second round of talks with Taliban officials on February 25 in Qatar, where they have their political office.
Shanahan replaced Jim Mattis as head of the Defense Department after Mattis resigned in protest to Trump's policies and left the job at the end of the year.
It was not immediately clear if Shanahan and Khalilzad would be conducting joint discussions during their trips.
Reuters meanwhile reported that Michael Kugelman, a South Asia specialist at the Woodrow Wilson Center, said Shanahan's main priority in Kabul should be to address Afghan government concerns.
U.S. troop numbers in Afghanistan since 2001. Since then, the administration has said it achieved a tentative "framework" for fuller peace negotiations with the Taliban.
However, he told reporters, he has no particular instruction from the administration about any slashing of the American troop presence in Afghanistan from the current 14,000 soldiers.
Instead they met directly with US negotiators in Doha last month for peace talks described by US President Donald Trump as "constructive".
However, the Taliban have put out contradictory information on what timeline the United States had agreed to in any potential withdrawal.
Trump has already said he is pulling out all 2,000 USA troops in Syria, where they have been aiding a Syrian Arab and Kurdish alliance fighting against the Islamic State and other insurgent groups.
Most recently, a Taliban official said no timetable had been agreed with the United States government for the partial withdrawal of USA forces.