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No best answer has yet been selected by badhorsey. Once a best answer has been selected, it will be shown here.
For more on marking an answer as the "Best Answer", please visit our FAQ.Department is singular. Therefore the correct sentence would be "The IT department HAS...." The same goes for "the Board", "the Company" "the Firm", but most people don't bother being so strict about it nowadays.
Also, we often use "they" when we don't know the gender of someone, or if the object they are discussing is neuter, e.g. a Department, I suspect this contributes to the spread of such constructions.
ursula62 is technically correct in saying that it should be "The IT department HAS..." but there should also be flexibility here.
Ask the Experts at Oxford is a brilliant website to explain such things and to point out where and when it is acceptable to use "have" instead of "has".
Basically, if by referring to the IT department, you really mean the members of the IT department, it is permissible to say "have".
For examples of this, see the following link:
http://www.askoxford.com/asktheexperts/faq/aboutgrammar/pluralverbs?view=uk
There is no rule except that of consistency. This is because there is no definitive body that rules on such matters of English language, the equivalent of the (boring and reactionary) French Academy in France. The "rules" evolve and alter all the time.
What there are are several helpful texts, such as Fowler's English Usage as well as "style guides" produced by businesses which work with words on a daily basis, such as the excellent one The Guardian newspaper has on their website and in book form. (The Guardian takes such collective nouns as singular, but they often make mistakes on such things.) However, whatever source you go to, the important thing is that you are consistent within your work. Don't use the singular in one paragraph and then a page later use a plural.
I think that the English language is a beautiful thing - it changes all the time, and many of these so called rules of grammar change too, fitting in with the way we are, not how we were in 1852. And yet, when a piece is well written, when it communicates what it sets out to do, we know it and appreciate it. It's good that badhorsey wants to write the right thing.