In October, the government brought in a new transitional law that means it is now up to individual clubs to decide whether police oversee matches.
The clubs and the state used to split the fees for a police presence in stadiums and it cost the public coffers around five million euros per season.
The new law has still to be fully ratified but Jose Gomes, the head of referees' association APAF, told Reuters it had already put referees on a knife edge particularly those starting out in their careers.
"Sending an 18-year-old to a pitch to spend 90 minutes fearing that if he gives a penalty or a red card that folks will jump him, is not good. We are very worried," he said.
"Fairness and freedom from bias are at stake."
Some Premier League and lower league matches have taken place with only stewards and other security personnel in attendance.
Top official Pedro Proenca threatened to pull out of refereeing one top-flight game between Vitoria Guimaraes and Vitoria Setubal.
"Referees going to those matches are not happy at all. That game in particular almost did not take place but in the end Proenca agreed out of his own goodwill," Gomes said.
There are around 5,000 referees in Portugal. Sitting in a humble office in downtown Lisbon, with walls draped by hundreds of club insignias, Gomes said he was pushing hard to find a solution to the problem.
"We hope to reach a compromise with the government. We even understand if we have to have less policemen at the matches," he explained.
"We want to negotiate ... if we are not heard we don't discard all forms of protest, including not refereeing matches, but that would be only in an extreme situation."
Portuguese referees have a good reputation with Proenca having been involved in the Euro 2012 finals and last May's Champions League final between Chelsea and Bayern Munich.
He was also voted the best referee in the world in 2012 by the International Federation of Football History and Statistics.
Gomes believes police-free matches could also be bad for Portuguese coaches, players and fans.
He said the cheaper alternative of using stewards and security officials was not safe because they were not as well-trained as the police and are not legally allowed to ask for identification or detain troublemakers.
"Proenca was assaulted at a match once when he was still refereeing in the third division a few years ago. He could have left refereeing for good because of this incident," added Gomes.
"He didn't. Otherwise we would have missed out on the best referee in the world ... what if we lose the next best because of this situation?"