The 31-year-old scored six goals in eight games for the club last season, but he has not started any of their previous three fixtures in the Premier League.
"He started the first two games and then I changed things around with different formations and different challenges. I just felt Bobby and Andy would help us in those games. So he's gone out of the team," Hughes told reporters.
"We know exactly what Djibril gives us. He's an outstanding finisher. As a team, we're strong and compact and we have enough quality about us to be able to release Djibril at the right time to show what he can do.
Cisse joined the R's from Lazio in January.