The man in his 50s, who cannot be identified in order to protect his daughter's identity, was granted bail at Queanbeyan Local Court on Tuesday.

The man is yet to enter pleas to 39 charges, including sexual intercourse with a person under 10, aggravated sexual assault, and assault with intent to have sexual intercourse with a person under 10.

His daughter was three years old at the time of the first alleged offence in the 1990s.

The offending allegedly took place over a 10-year period in several regional NSW locations.

The man, who has held senior management positions in a successful career, was arrested on September 27 and spent five days in custody before being granted bail.

The prosecution opposed bail because of the seriousness of the charges, but Magistrate Michael Antrum found the man's lawyers were able to show cause for his release.

Mr Antrum said he took into account that the man had an offer of employment as a chief executive officer, which he would lose if he remained in custody during what were likely to be lengthy court proceedings.

He also said the man had strong community ties and no criminal history.

"I'm not really concerned about failure to appear [in court]," Mr Antrum said. "He has real reason to remain in the jurisdiction."

Mr Antrum said he was concerned the man might endanger the safety of the alleged victim, interfere with prosecution witnesses or commit serious offences.

To allay those concerns, Mr Antrum set bail conditions including that the man not contact any prosecution witnesses other than through legal representatives, and that he surrender his passport and not travel outside NSW or the ACT.

He must also reside at the address given to the court and report to police weekly.

"A breach of any of these conditions would likely result in you being placed back into custody," Mr Antrum warned the man.

The case will return to court in December, when the prosecution will serve its brief of evidence.