Jonathan Roth pleaded not guilty to insurance fraud, conspiracy and falsely reporting an incident.
During his brief court appearance Tuesday, a judge set bail at $10,000 bond or $5,000 cash. His next court date is scheduled for Thursday.
Speaking outside the courthouse Tuesday, Roth's girlfriend of two years, Kristi Mayleas, said it is unlikely that he will be able to post the bond.
"He's just scared and really upset and mad at his dad for throwing him into this," Mayleas told CBS 2's Kathryn Brown. "He really thought his dad drowned."
Jonathan Roth has insisted he had nothing to do with his father's disappearance. Mayleas also said Jonathan Roth is innocent. Mayleas was the only one in court supporting and defending Jonathan Roth.
"His dad should be the one arrested and Jon shouldn't be arrested," said Mayleas.
Mayleas said Jonathan truly believed his father drowned.
"I've seen him cry, body shake. I don't know how you can fake those reactions," Mayleas said. "If I thought he was guilty I wouldn't be standing here. I wouldn't be standing by his side."
Prosecutors, however, claim the 22-year-old was involved in an alleged scheme with his father, 47-year-old Raymond Roth, to obtain more than $50,000 from life insurance policies.
It is believed that Raymond Roth is now back on Long Island. Sources told CBS 2's Sean Hennessey that Roth is in the psychological ward of a local hospital undergoing a mental evaluation.
The Nassau County District Attorney's Office said their plan was for Jonathan Roth to try to file a claim on July 31.
WCBS 880's Sophia Hall reports
But prosecutors said that was a lie.
"The defendant at all times was fully aware that his father never walked into the water and had in fact driven off in his personal vehicle," the complaint states.
That 911 call from Jonathan Roth triggered an intense air and water search that cost tens of thousands of dollars. While no one actually saw Raymond Roth swim away, the Massapequa man was initially presumed drowned.
But days later, Raymond Roth was found alive in Florida. He was then pulled over for speeding in South Carolina and told the officer, who noticed Roth was on a national registry of missing people, that he was on his way back to New York, police said.
Since being discovered alive, Roth has called and texted his wife, but hasn't come face to face with his family or with investigators, who are still looking for him.
Meanwhile, details of the alleged scheme continue to unfold.
At a news conference last week, Raymond Roth's wife Evana, said she was planning her husband's funeral when she discovered e-mails between father and son which sent instructions on what to do about money and the house.
"Jonathan, there needs to be a way for me to find out how things are going. Call me Sunday night at 8 p.m. at the resort. You cannot call from your phone," Evana Roth's attorney, Lenard Leeds, read from one of the e-mails. "I need to get to the bank for cash for the trip."
1010 WINS' Carol D'Auria reports
Evana Roth said she then showed the e-mails to her husband's brother, who called police and told them Raymond Roth was in Florida. She also said her husband withdrew about $10,000 from her bank account and had tripled his life insurance policy since January.
"The e-mails that I found are kind of self explanatory," Evana Roth said.
Mayleas said her boyfriend never received incriminating e-mails from his father that suggested the two were in cahoots.
"He looked into his account and said they weren't there," Mayleas said, referring to the alleged e-mails. "Jonathan didn't write the e-mails. The e-mails were sent from Raymond to Jonathan."
Neighbors said they don't know who to believe.
"They had to know -- you go to beach...wallet there and drivers license not there -- just doesn't add up," neighbor Ron Christian said.
Jonathan Roth was arrested on Monday. Prosecutors said it was then that he "admitted that his report was false," according to the complaint.
"On July 28, 2012, the defendant knew that his father was not missing because he observed him leave Jones Beach after informing the defendant that was going to flee secretly to Florida," prosecutors said.
Both Jonathan Roth and Evana Roth have accused Raymond Roth of being verbally abusive through the years.
"He's threatened to kill himself, according to Jonathan," Leeds said Monday. "He's threatened to kill Jonathan and Mrs. Roth, says that he's an alcoholic, he may be using drugs, and she's very concerned because of that."
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