The controversy surrounding Ran Baratz erupted as Netanyahu prepares to meet Obama in Washington Monday as part of efforts to heal rifts over the Iran nuclear deal, among other issues.
Netanyahu's office announced Baratz's appointment as the premier's head of public diplomacy and media on Wednesday, and Israeli news sites have since dug up a string of comments he has made.
In March, Baratz wrote about Obama on his Facebook page after Netanyahu addressed the US Congress to express opposition to the Iran deal. The speech drew heavy criticism from Obama.
"Obama's way of speaking about Netanyahu's speech -- that is the modern face of anti-Semitism in Western and liberal countries," Baratz wrote.
"And that comes, of course, with much tolerance and understanding toward Islamic anti-Semitism."
Netanyahu condemned the remarks Thursday, while Baratz apologised.
"They are inappropriate and do not reflect my positions nor government policy," the premier posted on Twitter. He said he would meet Baratz after he returns home from the United States.
Baratz said they "were written without thinking and sometimes as jokes in language which is appropriate for social networks and for a private person."
White House spokesman Josh Earnest said it was "readily apparent that that apology was warranted."
Secretary of State John Kerry -- who was also among Baratz's targets -- spoke with Netanyahu about the matter by phone Thursday.
Baratz's comments "were troubling and offensive," State Department spokesman John Kirby said.
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"We obviously expect government officials from any country, especially our closest allies, to speak respectfully and truthfully about senior US government officials," he added.
Besides his comments on Obama, Baratz reportedly wrote that Kerry's "mental age" was no older than 12.
He also spoke of Israeli President Reuven Rivlin in withering terms, saying that even the Islamic State group would not want him as a hostage.
Baratz recently wrote on Facebook that Rivlin, whose position is mainly ceremonial, was "such a marginal figure" that he had nothing to fear.
"We could send him by paraglider to the Syrian Golan controlled by ISIS" and they would want to send him back, he wrote.
Rivlin's office has reportedly asked Netanyahu's office for explanations regarding the comments about him.
In addition, the 42-year-old resident of a Jewish settlement in the occupied West Bank supported calls in 2004 for the construction of a new Jewish temple at the extremely sensitive Al-Aqsa mosque compound in Israeli-annexed east Jerusalem.
Both Jews and Muslims revere the compound as sacred. Jews are allowed to visit but not pray there to avoid provoking tensions.
Clashes between Israeli police and Palestinians at the compound in September preceded a recent wave of deadly violence that has provoked fears of a full-scale Palestinian uprising.
Baratz's appointment is to be submitted for cabinet approval, and some ministers have said they will oppose it.
Social Equality Minister Gila Gamliel said the comments "undermine the symbols of our government and those of our greatest ally, and may be misconstrued as an official stance," according to Haaretz newspaper.