"It would be useful and timely to reflect carefully on the period of time people are held in Identification and Expulsion Centres," Napolitano wrote in a letter delivered to the Ponte Galleria holding centre outside Rome.
Detainees at Ponte Galleria have rioted, sewn their lips together in protest at being held there for five months or more and several wrote to Napolitano and Pope Francis.
In his reply, 88-year-old Napolitano expressed "understanding of the suffering and pain of those who wrote as well as their requests and hopes".
The letter was delivered to migrants by centre-left Italian senator Luigi Manconi, writers Elena Stancanelli and Christian Raimo and actor Ricky Tognazzi.
Napolitano cautioned that he could not personally intervene in individual cases but said that the issue needed "debate in the country and in Parliament".
A total of 169,126 migrants were detained in Italy's migrant identification and expulsion centres between 1998 and 2012 of whom less than 50 percent (46 percen) were eventually deported, according to data from Catholic charity Caritas.