Holder was responding to questioning from Sen. John Cornyn (R-Texas), who suggested that the prosecutors handling the case were overzealous and guilty of misconduct.
In 2011, Swartz was charged with breaking into a computer network at the Massachusetts Institute of Technology and downloading 4.8 million documents from JSTOR, a subscription service for academic articles.
Swartz was an accomplished programmer and activist who argued that more online information should be free to the public.
Critics, including Swartz's family and members of Congress, have accused prosecutors of seeking excessive penalties in the case.
"Does it strike you as odd that the government would indict someone for crimes that would carry penalties of up to 35 years in prison and $1 million fines, and then offer them a three month prison sentence?" Cornyn asked.
Holder insisted that the charges themselves are less important than the penalties sought by prosecutors and said several months in prison would have been appropriate based on the crime.
But Cornyn worried that such harsh potential penalties could empower prosecutors to "bully" defendants into pleading guilty.
Cornyn urged Holder to respond in writing to a letter he sent in January, demanding detailed answers to a series of questions on the department's handling of the case.
Holder said the department has conducted a "good examination" of the case, including speaking with the prosecutors and the U.S. attorney who brought the charges.