Among the dead were 38 children and 132 women, the spokesperson, Asghar Jahangir, said.
The death toll was a sharp increase from a previous Iranian health ministry tally of 610 killed in Iran before a ceasefire went into effect on Tuesday last week.
Jahangir also revised the number of people killed in an Israeli strike on Tehran’s Evin Prison to 79, up from 71.
Israel launched the air war on June 13, attacking Iranian nuclear facilities and killing top military commanders as well as civilians in the worst blow to the Islamic Republic since the 1980s war with Iraq.
Iran retaliated with barrages of missiles on Israeli military sites, infrastructure and cities. The United States entered the war on June 22 with strikes on Iranian nuclear facilities.
Foreign Ministry spokesperson Esmaeil Baghaei said Israel’s “act of aggression had led to many war crimes”. He said Iran would transfer evidence to international organisations which he said should hold Israel to account.
“The Zionist regime’s (Israel) action was done without any reason or justification, therefore we do not believe in separating military and civilian (victims),” Baghaei told reporters at a regular press briefing.
He said any “martyr or destroyed building is an example of war crimes.”