AFL.com.au understands Duigan, 29, signalled his intention to retire to the Blues soon after returning to training last month.
But Duigan delayed making his decision public as uncertainty surrounded whether Carlton would be able to replace him on its senior list for 2014.
From snack to attack: Duigan's last-minute call-up
The South Australian informed the Blues he wanted to retire after the list lodgement deadline that would have allowed Carlton to replace him at the NAB AFL Draft or the Pre-Season Draft.
It is believed Carlton recently approached the AFL and inquired about placing Duigan on its long-term injury list next year and elevating a rookie to the senior list in his place.
The AFL has yet to rule on the Blues' request.
Duigan is desperate to see that Carlton not be left a player short next season because of his decision and has toyed with the idea of playing on if need be.
But AFL.com.au understands the defender did not leave for the Blues' training camp in Arizona with the rest of the team on Tuesday.
The defender's desire to retire has also been influenced by the likelihood he would struggle for senior opportunities in 2014.
In Mick Malthouse's first season as coach last year, Duigan played just five games after playing 38 in his first two seasons.
However, he memorably came in as a late replacement for the Blues in their elimination final against Richmond and starred in an unfamiliar role up forward, kicking four goals in Carlton's stirring 20-point win.
Duigan played 43 games in three seasons with the Blues after being a surprise mature-age selection in the 2010 NAB AFL Draft at pick 70.
At the time, Duigan had just completed a Master's degree in psychology and intended to work in Sudan for a year with his girlfriend as a volunteer.
Carlton is expected to make a statement on the defender's future shortly.
Nick Duigan is out of favour and struggling, but he doesn't want to leave Carlton short. Picture: AFL Media