The decision came a month after moderate President Hassan Rowhani took office with a promise of greater tolerance on social and cultural issues.
The culture ministry ordered the House of Cinema, which counts 5,000 members of all movie professions, to be dissolved in January 2012.
It was accused off having modified its founding statutes by deleting an adherence to the Islamic republic's constitution without consulting officials.
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Authorities say the union tends to politicise certain events, notably an annual film festival during which critical views are expressed of Iran's leaders.
Deputy Culture Minister Hojatollah Ayoubi, speaking at a reopening ceremony, said the decision was a sign of Rowhani's support for the film industry, ISNA news agency reported.
Ayoubi also criticised the previous administration for having politicised the closure.
"When a cultural issue -- like the one about the House of Cinema -- becomes a political one, that is (because) the situation was not managed properly," Ayoubi said.
The closure provoked criticism from several prominent Iranian directors, including Asghar Farhadi of the Oscar-winning movie "A Separation."