Federal prosecutors say 26-year-old Matthew Keys provided the hacking group Anonymous with login information to access the computer system of The Tribune, the Times' parent company.
According to the indictment handed down last week, a hacker altered a Times article posted in December 2010.
Keys posted on Facebook late on Wednesday that he "did not give a username and a password to anyone". He also said he did not conspire to damage a protected computer or cause transmission of malicious code, as the indictment states.
Reuters hired Keys in 2012. He has been suspended from his job.