Taxpayers are footing an annual bill of 659,294 for the unreturned books with 129,450 disappearing from the shelves.
The 2009 bill, revealed through the Freedom of Information Act, is nearly three times the previous year's 223,463 library book debt.
Edinburgh-based Rowling's Harry Potter books have slipped from the top spot to sixth in the most-stolen list.
Thieves have instead been taking work by the likes of children's author Wilson, American thriller writer James Patterson and romance novelist Nora Roberts.
More books were unreturned at Scottish Borders Council libraries than anywhere else last year. The authority cannot account for 11,918 books.
A new security tagging system has been introduced, according to the Borders Council's records manager Teresa Maley. She said: "All books are bar-coded so can be traced in the Library Management System.
"Proactive action is taken to try to recover books and we still ask for proof of identity and address when people join the library. If borrowers do not respond to library overdue notices, long overdue items are followed up using a materials recovery service."
Aberdeenshire Council, which lost 1,171 books, claims it has a library system that checks stock every day to keep thefts to a minimum.
A spokesman said: "A method of monitoring stock is the daily shelf list. This is a report that gives staff in a library a list of items that are requested in other branches.
"If an item cannot be found there is a process in place that allows the status of an item to be changed to missing.
"Most of these missing items are located in other areas of the library service, but on the odd occasion some of these items will be assumed missing for good."
New book theft prevention methods were introduced in West Lothian last year to tackle their 49,754 of missing stock. They have drafted in a debt collection agency to try to balance the books.
Police were called in to investigate a theft last year from a library in East Renfrewshire, where 3,713 books went missing last year, costing 28,389.
A spokesman said: "There was one incident in 2009 where the police were involved, but this was to do with customers who were attempting to steal materials from the library rather than borrow and not return them. Security gates have been in place in two libraries for several years."
1. Jacqueline Wilson
2. SQA school books
3. James Patterson
4. Francesca Simon
5. Nora Roberts
6. JK Rowling
7. Enid Blyton
8. Julia Donaldson
9. Matt Groening
10. Jodi Picoult
11. Stephen King
12. Stephenie Meyer
13. Irvine Welsh
14. Ian Rankin
15. Roald Dahl