Berbatov's agent has already confirmed the Bulgaria striker is "not happy" at Fulham and will seek a transfer in the January window.
But centre-back Hughes admits Fulham must do all they can to retain one of their top talents.
Berbatov's through-ball handed Fulham their goal in 2-1 defeat to Spurs on Wednesday night, Ahskan Dejagah finishing coolly past Hugo Lloris.
The Craven Cottage men could not claim victory though, extending their run of league defeats to six.
Tipping Berbatov to continue to uphold great influence on Fulham despite hankering for an exit, Hughes said: "He is a vital player for us.
"You have seen in his performance last night the role and the contribution he has in our team.
"We need all of our players performing at the highest levels they can.
"Those performances are brilliant for us, not only on the ball, but his work rate and not making it easy for their midfielders.
"He played a big part in the performances last night."
Spurs hit back for victory with goals from Vlad Chiriches and Lewis Holtby, flooring Fulham who had led past the hour mark.
The Cottagers host Aston Villa in west London on Sunday, seeking their first win under the sole control of Rene Meulensteen.
Hughes called on the Fulham squad to shoulder some of the burden for Martin Jol's exit.
He said: "When results are not good everyone looks at the manager but the players have to take responsibility as well.
"It is very easy to point fingers and blame others but we wanted to stick together and show we are still there fighting.
"With the performance we put in, we might have been unlucky not to get something.
"We wanted to make sure we had a performance with a lot of energy
"That is what has been disappointing over the last few games, sometimes the energy levels were not there.
"It took two good strikes to undo us last night.
"We are disappointed we have not got anything but there are obviously a lot of positives to be taken from the game."
Demanding Fulham keep focus as the new managerial reign takes effect, Hughes said little has changed since Dutchman Jol's departure last weekend.
He said: "When you have been in football for a certain amount of time, you get used to things like that happening.
"We can't do anything about it, we have just got to keep going, which we did.
"As far as on the training pitch, nothing really has changed too much because Rene had been in to help before.
"The old manager left and there have been a few little distractions but we spoke about keeping our focus."