Ibrahim Lawal Uwais, who is in his 40s, reportedly travelled to join the terrorist group fighting in Syria and Iraq, with his two wives and four children.
Justice Uwais was Nigeria's chief justice from 1995 to 2006.
Family sources told Daily Trust on Thursday that they were worried about the development even though Ibrahim is an adult.
An online newspaper, TheCable, quoted sources saying the former CJN's son travelled to Syria through Turkey, which shares border with the war-torn country.
Turkish embassy in Abuja confirmed that it issued visas to Ibrahim and his family members, the online newspaper said.
The details of his arrival in Turkey were made available, while images of CCTV recordings were also said to have been analyzed by the Turkish security agencies to establish their movement, according to the The Cable.
The terrorist group has annexed some parts of Syria and Iraq under its so-called Islamic State, where it summarily executed people including women and children.