The government said that the dispute, between the Greek Football Federation (EPO) on the one hand and the Super League and some clubs on the other, had led to a tense atmosphere which had prompted public safety concerns.
The decision could put Greece at risk of being suspended from international football by global soccer body FIFA and its European counterpart UEFA.
FIFA's statutes do not accept government interference of any kind in its member soccer federations and it had previously threatened to suspend Greece in April when the government ordered the Greek Cup final to be cancelled.
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"Based on the recommendations of the Chief of the Greek Police, Deputy Sports Minister Stavros Kontonis signed the order to postpone the start of the Super League until September 5, 2016," a government statement said.
"The reasons are the increasing conflict and extremely tense atmosphere which has developed recently between the Super League, the EPO and a significant number of clubs."
Last Friday, three of Greece's top clubs - Panathinaikos, AEK Athens and PAOK Salonika - said they would withdraw from the championship because the EPO had compiled the list of referees for the season without consulting them or the Super League.
Panathinaikos said they would not take part "in another championship scarred by dubious refereeing" and AEK described the situation as "a criminal theatre of the absurd surrounding Greek football".
FIFA could not immediately be reached for comment.
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