Eldine Baptiste, who is a member of the West Indies Cricket Board's selection panel, will take temporary charge of the team while the issue is investigated.
Simmons reportedly said there was "too much interference from outside" in the selection of the ODI squad, after all-rounders Dwayne Bravo and Kieron Pollard failed to make the cut.
According to cricinfo.com, Simmons said he and chairman of selectors Clive Lloyd were outnumbered 3-2 in a vote for the return of Bravo and Pollard.
"I think it's disappointing from the fact that I haven't got the best 50-over ODI squad that we can select in the Caribbean," Simmons was quoted as saying at a news conference on Wednesday by cricinfo.com.
A statement from the WICB on Monday said Simmons's comments "appear to question the legitimacy of the selection process" of the ODI squad.
The ODI series against Sri Lanka starts November 1 and is the first under new captain Jason Holder. Before that the teams play two Test matches.
Simmons, a former national team player, was in-charge of the West Indies since March.
Image: Phil Simmons
Photograph: Michael Steele/Getty Images