Marisha, can I give you my experience and point of view?
I run a website based database with a couple of hundred users entering technical data (some by keystroke entry, some by auto uploads) - this data is used in live individual and group analyses on the website that they can all access before I ever have a chance to correct their stuffups. It's bloody scary. But at the same time if that data were not immediately uploadable and accessible to them, I would not have a successful marketable product.
I've spent 10 years building offline databases with data submitted to me, entered by me, reports produced by me and then fed back to the clients. As powerful and perfect and valuable as those services were, they always limped along. They just couldn't produce the sense of ownership or immediacy that the online user-run system can.
The challenge then, for me, is to make the system safe.To push my own limits and knowledge to make it work the way it needs to work, rather than the way I currently know how to make it work.
To produce a system that is explicit and prescriptive in the way clients set up their data, and yet simple enough that the computer-phobes among them can feel in control.
That's the challenge I accept. And it means that as the system grows and confidence in it grows and more people are coming to me and saying 'hey, can we....?', I'm learning something new just about every darn day 0 - even after 10+ years designing databases, even after 3 years or so writing mysql and php.
My Point of View
1) It is not a good idea to do it through a website. If the data is incomplete or wrong I have to write the whole validation logic in Php which is a waste of effort
If I may say so, that sounds like fear talking to me. It sounds like you aren't confident of being able to build it.
If, as I take it from your post, this is data from more than one source and this is an ongoing requirement, then it is absolutely worth the effort to build a system for this. There's no question it is more input up front, but if it's an ongoing situation it is absolutely worthwhile.
We'll help you. You get to do the work, but we can guide and help troubleshoot.
Brotherhood of LAN has hit the nail on the head with LOAD DATA INFILE. jmccormac is bang on with his comments too.
..... of course I may have completely missed the point, in which case apologies. :)