The government was represented by Education, Lifelong Learning and Religions Minister Anna Diamantopoulou and culture ministry general secretary Lina Mendoni.
"Today we say goodbye one of the great artists of the globe, a man who broke away from the borders of the country and brought Greek culture to the ends of the earth through his work in film, the theatre and opera," Diamantopoulou said at the funeral.
In her funeral address, Mendoni spoke of a "friend" and "wise advisor" and a man with an "explosive temperament, abundance of energy, a restless and wakeful mind".
Also among those gathered to pay their last respects to Cacoyannis was Justice, Transparency and Human Rights Deputy Minister George Petalotis, who stressed that he felt honoured to get to know Cacoyannis in person.
Others attending the funeral included Democratic Alliance party leader Dora Bakoyannis, former minister Vasso Papandreou, Grigoris Psarianos, Mikis Theodorakis, Grigoris Valtinos, Katia Dandoulaki, Manousos Manousakis and Dimitris Papaioannou.
The Cyprus-born film maker is best known abroad for the 1960s classic film "Zorba the Greek" starring Anthony Quinn. He died on Monday at the age of 89.
He was nominated five times for an Academy Award (Oscar), receiving the Best Director, Best Adapted Screenplay and Best Film nominations for 'Zorba the Greek' and two nominations in the Foreign Language Film category for 'Electra' and 'Iphigenia'.
Another of his major hits was the film "Stella" starring Melina Mercouri, which was screened at the Cannes Film Festival and is considered one of the five greatest Greek films of all time.
Cacoyannis worked on many occasions with renowned Greek actress Irene Papas, teaming up with her in 1971 for the film 'The Trojan Women' starring Hollywood legend Katharine Hepburn, and was a close friend of Darryl F. Zanuck and George Cukor.
A pioneer of post-war Greek cinema and director of international hits, Cacoyannis refused a career in Hollywood, opting for quality theater. He also founded the Michael Cacoyannis Foundation for the study and support of the film and theater arts.