Nicolas Maingot, his deputy, has been named as an interim replacement for De Gregorio.
De Gregorio, who Fifa said will continue to serve "on a consultancy basis" until the end of the year, had been in the position since 2011 and was present when president Sepp Blatter announced his resignation on June 2nd.
"Walter has worked incredibly hard for the past four years and we are immensely grateful for all he has done," Fifa Secretary General
Jérôme Valcke said in the statement.
"I am glad we will be able to continue to draw on his expertise until the end of the year."
Football's governing body has been in the grip of a crisis since the end of May when 14 current or former Fifa officials and sports marketing executives were charged following a wave of arrests in Zurich, Switzerland as part of a US investigation into alleged corruption.