I'm not a CIL expert, but if the fees are essential to the delivery of the project, I see no obstacle to using CIL in this way.
Paragraph 59C of the Community Infrastructure Levy (Amendment) Regulations 2013 includes the following:-
"59C. A local council must use CIL receipts passed to it in accordance with regulation 59A or 59B to support the development of the local council’s area, or any part of that area, by funding—
(a) the provision, improvement, replacement, operation or maintenance of infrastructure; or
(b) anything else that is concerned with addressing the demands that development places on an area."
That's quite a broad definition. As a final check, ask your local planning authority.