He was refused bail amid allegations that he raped and repeatedly molested the girl at their home in south Belfast.
The 47-year-old, who cannot be named for legal reasons, was arrested after police were alerted last month.
A detective told Belfast Magistrates’ Court: “The injured party disclosed that she had been sexually abused by her father, the defendant, over the past 18 months.
“She said it happened at their home address while her mother was out at work.”
The accused faces nine charges, including rape, sexual assault and inciting a child to engage in sexual activity.
During police interviews he made no comment to questions, the court heard.
Forensic evidence and an evidential account from the alleged victim, now aged 16, have been obtained as part of the investigation.
The detective claimed that if released the man could flee or interfere with witnesses.
“The defendant has asked for contact with his children while he’s been in custody,” she added.
Defence solicitor Pearse MacDermott argued that his client should be presumed innocent and could surrender any passports to ease concerns.
Mr MacDermott also stressed: “There is no indication that he has made any threats or attempted to get the injured party to change her statement.”
Denying bail, however, District Judge Anne Marshall said: “These are serious allegations and I don’t think he is a suitable candidate.”
She remanded the accused in custody, to appear again by video-link on February 23.