This gives continued special intervention powers for the police and army.
Extensions of the state of emergency – which has been in place since January 2011, when a revolution ousted long-time president Zine al-Abidine Ben Ali – had only been made for 30 days at a time since July.
Authorities pointed to the shortened extensions as a sign of improving security, but Wednesday's announcement of a three-month extension will likely raise fears of a deteriorating situation in Tunisia, which is still dealing with instability unleashed by the revolution.
"Marzouki decided on Wednesday to extend the state of emergency by three months from November 1 2012," said the official TAP news agency on Wednesday.
The extension was proposed by military and security officials, it added.
The announcement comes after a series of attacks by radicals in recent weeks.
The authorities have vowed to crack down on Islamist violence in the wake of a Salafist-led attack on the US embassy in September in which four assailants were killed.
On Tuesday, extremists raided two national guard posts in a Tunis suburb, leading to clashes with security forces that killed one attacker, the interior ministry said.
After the clashes, dozens of radicals, some armed with knives, took to the streets of Tunis on Wednesday.
Government vs opposition
The government said police and soldiers had deployed heavily and would use all means to quell any unrest, but no such forces were visible on the ground.
Tuesday's attacks in the Tunis suburb of Manouba came after police arrested a Salafist suspected of assaulting the local security chief.
The opposition accuses the government, led by Islamist party Ennahda, of failing to rein in violence by the Salafists, a hardline branch of Sunni Islam.
Ennahda issued a statement on Wednesday appealing for calm and saying the "state has a right to deal with all threats to social peace." – Sapa-AFP