Netanyahu had reportedly been working with the State Department “for a number of months” on the shift in policy.
A 2015 law mandates periodic reports on anti-BDS actions taken by diplomats.
The deletion as an area under the aegis of its Near East Bureau does not constitute a change in U.S. policy, a spokeswoman said.
“It is inconceivable he got security clearance twice,” his former boss said. “I’m horrified Gebert worked for me at the State Department.”
The employee allegedly hosted white nationalist meetings at his home and attended an invite-only dinner with Holocaust denier David Irving.
An official argued that the change did not signal a shift in State Department policy.
There has been no anti-Semitism monitor since President Trump assumed office in January 2017.
A number of liberal Jewish groups had called on the Senate to reject Pompeo, in part because of his past remarks about Muslims.
The position of Special Envoy to Monitor and Combat Anti-Semitism has not been filled since Trump was inaugurated.
A State Department official said in January that the Trump administration considers the position “crucial” — but it still hasn’t named a leader.