One list Fifty Shades of Grey was perhaps destined to be among was books most likely to be removed from school and library shelves in the US.

On Monday, E L James's multimillion-selling erotic trilogy was placed No 4 on the American Library Association's annual study of "challenged books". These are works subject to complaints from parents, educators and other members of the public. Objections are based on criteria such as offensive language, and, of course, graphic sexual content.

Top of the list was a not a story of the bedroom, but the bathroom, Dav Pilkey's Captain Underpants books (offensive language, unsuited for age group), followed by Sherman Alexie's prize-winning The Absolutely True Diary of a Part-Time Indian (offensive language, racism, sexually explicit), and Jay Asher's Thirteen Reasons Why (drugs/alcohol/smoking, sexually explicit, suicide). Also on the list, at No 10, Nobel laureate Toni Morrison's Beloved (sexually explicit, religious viewpoint, violence).

"It's pretty exciting to be on a list that frequently features Mark Twain, Harper Lee, and Maya Angelou," Pilkey said in a statement. "But I worry that some parents might see this list and discourage their kids from reading Captain Underpants, even though they have not had a chance to read the books themselves."

The library association's Office for Intellectual Freedom defines a challenge as a "formal, written complaint filed with a library or school requesting that a book or other material be restricted or removed because of its content or appropriateness." The office received 464 challenges last year, an increase of more 25% from 2011, but still low compared to the 1980s and 1990s. Exact numbers, including how many books were actually pulled, are hard to calculate. The association has long believed that for every complaint registered, four or five go unreported by libraries, and that some librarians may restrict access in anticipation of objections.

"One reason we think the number went up in 2012 is that we made challenges easier to report by including a portal on our web page," said Barbara M Jones, director of the OIF.

The challenged books list was included in the library association's annual State of America's Libraries report that examines how libraries are responding to budget cuts and the financial advice they offer for patrons during hard economic times.

The Fifty Shades books were released last spring, and public libraries in Georgia, Florida and elsewhere soon pulled the racy romance trilogy or decided not to order the books, saying they were too steamy or too poorly written. Local library representatives at the time denounced the novels as "semi-pornographic" and unfit for community standards.

But the list also included some works highly regarded in the literary community: Morrison's Beloved, winner of the Pulitzer prize; Alexie's novel, a National Book award winner; and a book club favourite, Khaled Hosseini's The Kite Runner (homosexuality, offensive language, religious viewpoint, sexually explicit). Young adult novelist John Green was on the list, for Looking for Alaska (offensive language, sexually explicit), along with perennial chart topper And Tango Makes Three, by Peter Parnell and Justin Richardson, the story of two male penguins who raise a baby penguin. Others on the list were Alvin Schwartz's Scary Stories (unsuited for age group) and Jeanette Wells's memoir The Glass Castle (offensive language, sexually explicit).

The Captain Underpants books, which Green said he's currently reading to his three-year-old son, have long been debated among parents and educators. Some praise the books because they encourage boys to read, others criticise them for their toilet humour and irreverent attitude; the title character is a superhero devised by two young students about their grouchy school principal, Mr Krupp.

"I don't see these books as encouraging disrespect for authority. Perhaps they demonstrate the value of questioning authority," Pilkey said. "Some of the authority figures in the Captain Underpants books are villains. They are bullies and they do vicious things."

Pilkey said his characters are based in part on teachers and head teachers he had – some of whom were villains who got away with it because they were authority figures.

"None of the children in my school, including me, thought to question them," he said. "So, I do feel there is real value in showing kids that not all authority figures are good or kind or honorable."

Challenged books are a measure of trouble, but also a measure of popularity, whether as a cause or an effect. Some famous entries from recent years have dropped off the top 10, likely a sign of reduced attention overall including JK Rowling's Harry Potter books, Stephenie Meyer's Twilight series, Suzanne Collins's Hunger Games trilogy. Jones thinks some publishers "love it when their book is mentioned" because of the attention it receives, while Green agrees that getting on the list "means lots of people are reading your book".

The president of Scholastic's trade division, Ellie Berger, said in a statement that the "appearance of Captain Underpants on the 2012 ALA list coincides with the publication of Dav Pilkey's first new Captain Underpants book in six years and the return of the series to national bestseller lists – both of which are evidence that this longtime bestselling series continues to inspire a love of reading (and underpants) for a new generation of kids."