Greek Cup cancelled after crowd trouble
In a statement, Kontonis announced the "definitive cessation" of the competition following "disturbance of the social peace and legal order".
He raised concerns about refereeing appointments for key matches and called on the country's football federation to provide "meaningful answers."
The game between hosts PAOK and league champions Olympiakos, who were also the cup holders, at Toumba Stadium in Thessaloniki was abandoned in the 89th minute with the visitors leading 2-1 after PAOK fans invaded the pitch and dozens of flares and smoke bombs were thrown from the stands.
PAOK fans were furious at their team being denied a penalty by referee Andreas Pappas which would have improved their chances ahead of the second leg in Piraeus, scheduled for April 6 or 7.
PAOK had earlier announced that they would not travel to Piraeus for the second leg unless a foreign referee was appointed.
Riot-trained police turned back troublemakers and made 15 arrests. Twelve police officers were injured, police announced, two of them needing hospitalisation.
There had already been trouble before kick-off as three arrests were made after PAOK supporters fought with police outside the stadium.
Olympiakos coach Marco Silva, who saw his side win a record 43rd Greek title at the weekend, was also struck in the back by a plastic cup during the second half.
"The government is closely monitoring developments and those who do not take seriously our actions must be aware that it will not hesitate to go directly into further decisions," Kontonis' statement added, leaving the door open to a suspension of the Greek Super League if violence continues.
Last year, Kontonis suspended Super League matches following violence between rival sets of supporters.
AEK Athens had been due to meet capital rivals Atromitos in the other semi-final, first leg, on Thursday. The final was scheduled for April 23.
PAOK face a heavy fine as well as the possibility of being forced to play matches behind closed doors.