Pilavios told Reuters he also expected the federation's general assembly to approve the banning of flares and firecrackers at Greek stadiums from next season.
"We are trying to make our disciplinary codes tougher and we will do that by excluding flares and fireworks," he said on the sidelines of the UEFA Congress.
"We want to have the help and contribution of the state and police and the clubs who have all the ultras [hard-core fans] who are creating this big problem."
The latest in a string of incidents saw AEK Athens goalkeeper Sebastian Saja hit by a flare thrown from the crowd in a match at PAOK Salonika earlier this month.
"The change has to be approved by the general assembly of the Greek federation in June and will come into force immediately," said Pilavios.
He was also hopeful that the government would introduce new sports legislation to try and stamp out hooliganism.
"We have to study the law and give our opinion, I think it will be in the right direction," he said.
"The surveillance systems have to be monitored better by the police and we hope to see some arrests in the stadiums."
Pilavios said he understood why players attempted to go on strike over the problem earlier this month.
"I understand what the players said, they wanted to give a message. but I don't think the strike is something that can solve the problems," he said.
"But I think we received the message."
Pilavios added that the problem was largely confined to domestic matches.
"Greek fans prove when they watch their teams play in Europe, and if they are convinced it's for their own good, they can do it and we have a good atmosphere."
