Paul van der Sloot, a judge-in-training on the island, was questioned for two hours Sunday afternoon after five hours Saturday night, said Police Superintendent Jan van der Straaten.
Joran van der Sloot, 17, one of the people last seen with Natalee Holloway the night she disappeared. Three other men have been detained, but no one has been charged.
Van der Straaten said the father was asked to come back Sunday because officials were not able to finish the interrogation on Saturday, but declined to give more details.
"He was questioned as a witness, no more or no less," van der Straaten told The Associated Press.
The attorney general's spokeswoman, Mariaine Croes, said witnesses are questioned when prosecutors believe they may be able to add something to the case.
"You may know something more or you may have seen something more, but you are not a suspect or thought to be part of any crime," Croes said.
"I think that he probably knows more than he's letting on," said Robin Holloway, the missing teen's stepmother, on CBS News' The Early Show.
"I was questioning the integrity of the father because he is a person that is currently in training to be a judge, but apparently his son feels that he is above the law," said Linda Allison, Holloway's aunt, also on The Early Show.
"You have a son that is out driving under the age of 18 and here, according to Dutch law, you have to be 18 to be able to drive, to gamble, to drink. And with him being 17 years of age, he's done all of those things," Allison told Early Show co-anchor Hannah Storm.
"I don't know if he would be arrested, but I would feel like he would at least know some key information as to when his son arrived home," she added.
During Sunday's interrogation, van der Sloot's wife, Anita van der Sloot, met with Joran in jail, said van der Straaten.
Holloway, 18, of Mountain Brook, Ala., disappeared in the early hours of May 30, the last day of a five-day vacation with 124 students celebrating their high school graduation. Her U.S. passport and packed bags were found in her room.
Joran van der Sloot and two friends said they took Holloway to a northern beach but dropped her off at her Holiday Inn, where they claim she was approached by a security guard.
On Saturday, a judge ordered Joran van der Sloot and his two friends, brothers Deepak Kalpoe, 21, and Satish Kalpoe, 18, to stay in jail for at least another week while the investigation continues.
CBS News Correspondent Kelly Cobiella reports that they have been moved to a prison on the southern end of the island where they'll stay for at least another week.