" I understand why there had to be a rise in fees. But £3,000 to £9,000 is such a drastic change, why not gradually move it up and let people prepare for what's going to happen?"

Can i use has to be instead of had to be? And what the meaning of had to be in the sentence above and in which conditions should we use had to be? Please give me good explanation.

Thank you!
Yes, you may use "has to be."

"To be" is "to exist."

"Had to" is "needed to."

"Has to" is "needs to."

It needed to exist then - when the rise in fees was decided upon.

It needs to exist now - the greater fee.

Notice the difference in the thing which must be:

In the past, a rise was needed.

Now that we have had the rise, we need to keep the higher fee.
Thank you for your continuos help Avangi.
Teachers: We supply a list of EFL job vacancies
So I can use either one of the phrase "has to be" or " had to be" in the above sentence right?
Yes. No problem.

Your choice of tense can shift the focus from the decision to raise the fee then, to the need to keep it now.