Press Association Sport understands veteran striker Nicky Forster has been placed in temporary charge at Griffin Park following the departures of Scott and assistant Terry Bullivant.
Former Bees boss Martin Allen has already been linked with a return to the club, possibly until the end of the season.
Fans were calling for Scott to leave following Tuesday night's 4-1 defeat at lowly Dagenham & Redbridge which left them two points above the npower League One relegation zone.
Scott, 38, took charge of Brentford in December 2007 and led them to the League two title in his first full season in charge.
The Bees finished ninth in League One last term but have struggled to recapture that form this campaign.
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