The difference of opinion has been most evident in Trump and Tillerson's views on the ongoing diplomatic fallout between the Saudi Arabia and Qatar.
SECRETARY TILLERSON: Great to see you again at the State Department.
Tillerson's absence coincides with a number of reports hinting at growing tension between the secretary of state and the president.
"He's got a lot of work", Nauert said.
"He's entitled to take a few days himself", she said.
The change in Tillerson's tone followed a stressful week for the secretary of state.
The rumors of a pending "Rexit" were first spread around by CNN last week, when the network cited sources out of the White House in claiming that the top United States diplomat was frustrated with Trump's different viewpoints on important foreign policy matters.
Tillerson spoke briefly with reporters before heading into a meeting with Qatari Foreign Minister Mohammed bin Abdulrahman al-Thani in Washington.
As rumors swirl that U.S. Secretary of State is considering leaving his post he reassures reporters at the State Department that he is "not going anywhere". "If that's what they want to do, fine: Someone will fix in a couple years, but in the meantime we're going to lose a lot of ground".
He's deeply engaged in that work، ABC News reported.
Nauert pointed out that Tillerson "does, however, serve at the pleasure of the President, just as any cabinet official would". Tillerson was supposed to clean house, but he left half of them in place and he hid the other half in powerful positions all over the building.
Two sources familiar with Tillerson's conversations with friends told CNN over the weekend that he has grown so frustrated with President Donald Trump and his administration that there may soon be a "Rexit".