Retired Marine general James Mattis was sworn in Friday as US defense secretary, praising intelligence agencies and calling for stronger ties with allies in a break from positions taken by President Donald Trump.

Mattis was confirmed by a 98-1 vote earlier Friday in the first action taken by US senators after Trump took the oath of office, and was sworn in by Vice President Mike Pence.

"Together with the intelligence community we are the sentinels and guardians of our nation," Mattis said in a statement to the Department of Defense -- tipping his cap to the agencies that Trump has sharply criticized as they investigate claims of Russian interference in the US election.

"Every action we take will be designed to ensure our military is ready to fight today and in the future."

"Recognizing that no nation is secure without friends, we will work with the State Department to strengthen our alliances," he said, a contrast to Trump's recent branding of the NATO military alliance as "obsolete."

Lawmakers passed a special waiver allowing Mattis, who retired in 2013, to serve before a customary seven-year limit on former military personnel assuming the Pentagon's top post.

John Kelly, another retired Marine general, was also confirmed and sworn in to head the Department of Homeland Security.

"These uniquely qualified leaders will immediately begin the important work of rebuilding our military, defending our nation and securing our borders," Trump said in a statement.

"I am proud to have these two American heroes join my administration."

Mattis has won accolades from both parties and many in the armed forces, and his path to Trump's cabinet was relatively uncontroversial compared to that of other nominees.

A cornerstone of US democracy is that civilians, not people in uniform, control the military, and the commander-in-chief is the president.

Some in Congress initially raised eyebrows because Mattis, a 66-year-old Washington state native, had only retired from active duty in 2013.

The waiver allowing him to take the top Pentagon post was only granted once before, for the famous World War II general George Marshall who served under President Harry Truman from 1950-1951.

Mattis is known as a colorful commander and famed for his pugnacious aphorisms. The media dubbed him "Mad Dog" for his battle-hardened swagger and the sort of blunt language Marines are famous for.

He has been quoted as saying, "Be polite, be professional, but have a plan to kill everyone you meet."

But Mattis also has a well-known cerebral side: he issued reading lists to Marines under his command, and instructed them that the most important territory on a battlefield is the space "between your ears."

While Mattis sailed through his confirmation, Democratic lawmakers are putting up stiff resistance to other Trump cabinet picks, including nominees to head the departments of education and health and human services.

Mattis replaces Ashton Carter, a longtime Pentagon bureaucratic warrior who served as former president Barack Obama's fourth defense secretary.