There is a great deal of information out there about this subject, so here are a few places to start, including a book written on the subject by the librarian who exposed the program which was called "The Library Awareness Program".
Hopefully you will be able to access the links below You can also search further with the term "Library Awareness Program" in seach engines or databases.
Ann, for Radical Reference
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http://www.aaas.org/spp/secrecy/Presents/foerstel.htm
Secrecy in Science: Exploring University, Industry and Government Relationships
Panel II: Remarks by Herbert Foerstel, former Head of Branch Libraries at University of Maryland and board Member of the National Security Archive.
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http://info.greenwood.com/books/0313267/0313267154.html
Surveillance in the Stacks The FBI's Library Awareness Program By Herbert N. Foerstel Political Science, Contributions in, No. 266 (ISSN: 0147-1066) Greenwood Press. Westport, Conn. 1991. 184 pages LC 90-38419. ISBN 0-313-26715-4. FFG/ $81.95
This book is by the librarian, same one as above, which exposed the Library Awareness Program. H has a new book out on PATRIOT.
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http://sunsite.berkeley.edu/GODORT/resolutions/880713774.html
http://www.dangerouscitizen.com/Articles/630.aspx
Government Documents Round Table (GODORT) passed a resolution against the Library Awareness Program. The second site appears to say that the ALA itself adopted the resolution but I'm not sure about that. I'm sure it's covered in Foerstel's book.
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The ALA has this site above, called "FBI in Your Library" which has a little history.