The ministry says most of the dead were Kurdish militants but the pro-Kurdish Peoples' Democratic Party (HDP) says 20 civilians were killed in the violence.
Locals say Cizre has been "under siege" since the military imposed a curfew.
On Thursday police stopped a delegation of HDP leaders who were trying to reach the south-eastern city on foot.
The group includes the party's leader Selahattin Demirtas and 30 members of parliament, who say they want to draw attention to what is happening in the mainly Kurdish area.
They were intercepted by police near Idil, 28km (17 miles) from Cizre.
Deadly clashes between Turkish forces and the militant Kurdish organisation, the PKK, have intensified since a ceasefire collapsed in July.
Turkish jets have bombed PKK bases in northern Iraq and the army has boosted security and imposed curfews across the south-east.
Mr Demirtas said the humanitarian situation in Cizre was worsening, with people unable to buy bread or access water.
The body of a 10-year-old boy killed in the violence was being kept in a refrigerator by family members because restrictions on movement meant they could not take him to the mortuary, the BBC was told.
Interior Minister Selami Altinok said the curfew would continue until the military operation was completed.
Mr Demirtas warned the country was heading towards civil war.
Turkish prosecutors are currently investigating the HDP leader for insulting the president.
They want to have the MP stripped of his parliamentary immunity.
Turkey is to hold new elections in November after inconclusive polls in June.
Separately, the interim government has deported a Dutch journalist.
Freelancer Frederike Geerdink, who was arrested on Sunday, was accused of links to the PKK.