Deborah Dugan was placed on administrative leave following an allegation of misconduct, the Academy said in a statement.
Dugan had replaced former chief executive Neil Portnow, who caused controversy in 2018 when he suggested female artists should “step up” if they wanted to be recognised at the Grammys.
She was the Academy’s first female president and, in an interview published this week, called her role “the best job on the planet”
In a statement, the Recording Academy said: “In light of concerns raised to the Recording Academy board of trustees, including a formal allegation of misconduct by a senior female member of the Recording Academy team, the board has placed Recording Academy president and CEO Deborah Dugan on administrative leave, effective immediately.
“The board has also retained two independent third-party investigators to conduct independent investigations of the allegations.”
It continued: “The board determined this action to be necessary in order to restore the confidence of the Recording Academy’s membership, repair Recording Academy employee morale, and allow the Recording Academy to focus on its mission of serving all music creators.”
Board chairman Harvey Mason Jr will step into Dugan’s role until the investigation reaches a conclusion.
He sent an email to members of the Academy on Thursday, assuring them that “the Grammy Awards and all related activities will go forward as planned”.
Dugan is a former lawyer and record executive who previously ran Bono’s charity Red, which works to combat Aids and other diseases in Africa.
According to Variety magazine, the 61-year-old had met with resistance in her attempts to modernise the Recording Academy, with one unnamed source calling her removal a “coup”.
The 62nd Grammy Awards are due to take place at Los Angeles’ Staples Center on Sunday 26 January, hosted by Alicia Keys.
Performers on the night will include Billie Eilish, Camila Cabello, Bonnie Raitt, the Jonas Brothers, Demi Lovato and Rosalía.