Adrian Lamo, 22, turned himself in to marshals at the federal courthouse in Sacramento, said FBI spokeswoman Karen Twomey Ernst.
He is charged with altering The Times' databases between February and April 2002, causing The New York Times Co. damages exceeding $25,000.
An FBI affidavit says Lamo added his name, cell phone number and e-mail address to The Times' op-ed contributor list and its administrative database, listing his area of expertise as "computer hacking, national security, communications intelligence."
The complaint also says Lamo obtained more than $300,000 worth of services from the LexisNexis electronic information service during the same period by accessing The Times' LexisNexis account.
Lamo kept using LexisNexis to, among other things, search for mentions of his own name and exploits, according to an affidavit.
After an afternoon court appearance, Lamo was released into his parents' custody on $250,000 bail and ordered to report to the FBI's New York office Thursday.
A federal defender who represented him during the brief appearance had no comment.
Lamo has acknowledged involvement in some dramatic computer break-ins over the past several years at large corporations such as Worldcom and ExciteAtHome. He also acknowledged changing the text of at least one news story on Yahoo's Web site in September 2001.
The New York investigation became public a year ago, when a federal prosecutor tried unsuccessfully to subpoena an MSNBC reporter's notes, e-mails and other information about conversations with Lamo.
Lamo frequently uses public computers at copy stores for his hacking activities as he travels the nation. He has offered to work for free with his hacking victims after each break-in to improve the security of their networks.
By Don Thompson