Hamid Hayat, 22, was accused of lying to the FBI earlier this month when he said he did not attend a terrorism camp in Pakistan in 2003 and 2004, prosecutors said.
His father, Umer Hayat, 47, was charged with lying to investigators when he denied that his son had attended such camps. The FBI said the elder Hayat later admitted to flying his son to Pakistan and paying for the camp, which was run by the friend of a relative.
The indictment said the younger Hayat falsely told authorities he was not involved with a terrorist organization, he never attended a terrorist camp and he had never received any weapons training at such a camp.
In an affidavit, the FBI said Hamid Hayat attended a terror camp for about six months before returning to the U.S. intending to wage attacks. They said they found no immediate threat of terrorist activity.
Defense lawyer Wazhma Mojaddidi said Thursday that Hamid Hayat "has most definitely never attended a terrorist training camp."
The Hayats, both U.S. citizens living in the farming town of Lodi, have pleaded not guilty and are being held without bail. They are scheduled to appear in court Tuesday.
The FBI spent several years investigating possible links to terrorism in Lodi, about 30 miles south of Sacramento.
Members of the 2,000-member Pakistani community there have said they have been harassed by authorities, and on Thursday two groups said they would file complaints.
In other developments, a 68-year-old Pennsylvania man who told undercover federal agents he had "no loyalty for America" was indicted Thursday on a single count of attempting to support al Qaeda by allegedly trying to build a bomb and sell it to the terrorist group or its affiliates.
If convicted, Ronald Allen Grecula, of Bangor, Pa., could face up to 15 years in prison and a $250,000 fine.
In Arkansas, a graduate student who allegedly told a professor that he was leaving to fight in a Palestinian holy war was in federal custody Thursday. Federal agents arrested Arwah J. Jaber on a criminal complaint accusing him of knowingly attempting to provide support to a foreign terrorist organization.