Matches were suspended on March 12, a day after Ivan Savvides, the president of PAOK, charged on to the pitch with a gun in his belt, to complain over a disallowed goal towards the end of a game against fellow title contenders AEK Athens.
Greece's Deputy Culture and Sports Minister Georgios Vassiliadis took the decision a day after Superleague clubs unanimously accepted changes to the league's disciplinary code and submitted proposals for improving the country's top soccer division.
"The Deputy Minister for Culture and Sport....has decided to immediately lift the suspension of the Superleague championship as well as the Greek Cup," the ministry said in a statement.
Greece had indefinitely suspended matches after Savvides was filmed wearing a gun holster as he strode on to the pitch to protest about a PAOK disallowed goal against AEK Athens.
The game was abandoned and later awarded to PAOK 1-0 following the controversial goal which had prompted the initial protests.
Savvides has since apologised for his actions but he and the club still face sanctions.
The Superleague disciplinary body is expected to announce its decisions on PAOK later this week, which could include a points reduction for the team and a stadium ban for its club boss.
All decisions, however, are not final and can be appealed.
Both PAOK and AEK are title contenders and any points reduction as part of PAOK's punishment could cost the northern Greek club the championship.
AEK are currently top on 54 points from 24 matches with PAOK in second place on 52 from 23 games.
World soccer's governing body FIFA has also warned Greece to act decisively in this matter or risk facing a potential national suspension.
A report on the state of Greek football by a monitoring group that visited Greece two weeks ago has been delivered to both FIFA and European body UEFA.
The European Club Association (ECA) has suspended PAOK as a member with immediate effect.
(Reporting by Karolos Grohmann,; Editing by Ed Osmond and Toby Davis)
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