Under Puerto Rican law Martin could face up to 50 years in prison if found guilty of incest.
Martin said in a tweet earlier this month that the order is based on "completely false" allegations and that he will face the process "with the responsibility that characterises me".
"I appreciate the innumerable gestures of solidarity and I receive them with all my heart," he wrote.
Martin's attorney Marty Singer told the New York Post that his client completely denied the allegations.
"Unfortunately, the person who made this claim is struggling with deep mental health challenges. Ricky Martin has, of course, never been — and would never be — involved in any kind of sexual or romantic relationship with his nephew," said.
"The idea is not only untrue, it is disgusting. We all hope that this man gets the help he so urgently needs. But, most of all, we look forward to this awful case being dismissed as soon as a judge gets to look at the facts."
The revelations come after Martin was hit with a $4.8 million lawsuit from his ex-manager Rebecca Drucker, with documents claiming he owes the sum after she helped resurrect his career and protect him from allegations that would have ended it altogether.
Drucker also claimed the Latin hitmaker was threatened and intimidated with a "potentially career-ending allegation" and she helped him emerge "unscathed" and proceed with his "professional resurgence".
SEXUAL HARM - DO YOU NEED HELP?
If it's an emergency and you feel that you or someone else is at risk, call 111.
If you've ever experienced sexual assault or abuse and need to talk to someone contact the Safe to Talk confidential crisis helpline on:
• Text 4334 and they will respond
• Email support@safetotalk.nz
• Visit https://safetotalk.nz/contact-us/ for an online chat
Alternatively contact your local police station - click here for a list.
If you have been abused, remember it's not your fault.
- Additional reporting, AP
