This is just my tuppence but I'd say by the sound of it you'd be better off not interfering with that main sewer. Would be fairly costly, depending on the size, and would be involving the council a lot more. You wouldn't, or shouldn't be allowed to build on top of it as is. Probably worth asking a local engineer for his opinion though.
Just re-read your post, if its only an access point that's in your way then its probable that the main sewer is outside this again, possibly outside your site boundary, in which case there should be no problem moving the access point. You can build on top of your own private connection no bother.