The 30-year-old signed a three-year deal with the Trotters when he moved to the Reebok Stadium from Watford for a reported £2m fee in August 2008.
Shittu made 12 appearances in his first season at Bolton, but he did not feature for the first team last season.
However, the centre-back was still named in Nigeria's 2010 World Cup squad and played in all three of their Group B games in South Africa.
Source: BBC Sport