There were just a lot of questions about his other relatives, some of whom he will never see again.
Habibie, 11, is the second tsunami victim to be reunited with his family with the help of Save the Children, one of many non-governmental organizations providing aid to survivors after the December 26 disaster.
The fifth-grade student had a matter-of-fact attitude when his father Jamil, 55, his eyes moist, embraced him.
"My son," said Jamil, a poor farmer.
"Father," was all Habibie said before the two sat down to exchange stories about the previous four weeks.
Habibie, the sixth of seven children, wanted to know the fate of his siblings and other relatives.
"Safe, safe," Jamil said as Habibie mentioned some names.
"What about older sister Ainul Mardia from Cot Paya village, where is she?" Habibie continued.
"She's not there anymore and neither is her baby daughter," Jamil replied.
"Where are they now?" asked the boy.
"We don't know yet because we haven't found their bodies," answered the father, whose youngest child also died in the tsunami.
Habibie was silent.
The boy, whose mother died several years ago, frequently stayed with Mardia in the village of Cot Paya, near Banda Aceh.
On the morning of the earthquake he was in Banda Aceh, staying at the home of friends. He said he survived the rushing water by climbing onto the roof of a house.
Jamil said that after he found his daughter's house levelled in Cot Paya he went to a camp where displaced people from her village were staying near Banda Aceh's airport.
By chance his brother Abdurrahman was looking for work at Save the Children's office and recognized the name Khairul Habibie among 72 youngsters on an agency list.
He said he then notified Jamil who went to the office and was interviewed to confirm he is Habibie's father. They were reunited on Friday.
Eileen Burke, Save the Children's spokeswoman, said Habibie was the second child to be reunited with his family. The first reunion was a week earlier.
People claiming to be parents are interviewed in great detail to verify their claim, she said.
"I believe we now have 10 more being verified. People have come forward and said this child on the list is my daughter or son or niece or nephew, and we are in the process of verifying the information," she said.
"I'm happy I can meet my father but I'm also sad because my sister, brother and niece aren't here anymore," Habibie told AFP before he set off with his father for the airport refugee camp, reluctantly leaving behind many friends at the house where he had been staying.
"Thank God one more of my children could be saved," Jamil said.