A spokesperson has said that "the law is very clear" and that it is an offence to organise or participate in a parade that has not been appropriately notified to the PSNI.
"Where a parade is not so notified and is therefore breaking the law, it is a matter for the police to deal with under the various options open to them that could include stopping the parade or gathering evidence for potential prosecution," the Parades Commission statement said.
After remarks made by senior Orange Order member, Reverend Mervyn Gibson, the clarification was issued.
The PSNI will stage a major operation in Belfast on Saturday, in what many see as a litmus test of the forthcoming marching season. There are two key events - the first official Orange Order parade - and a Union flag protest outside police headquarters.
It will come after Rev Gibson told BBC NI's The View that the Orange Order may consider no longer giving police notice for their parades.
He said the organisation was considering the step after loyalist flag protests have been ongoing without any notice to police or the commission.
The parades watchdog said it has been notified of around 30 flag protests so far, and noted one event in east Belfast they had not been told about.
However protestors have marched into Belfast city centre each weekend without any notification to police- meaning the commission does not have the legal powers to rule on these parades.
In a tactic change, protestors have also held a number of white line pickets, which can also be held legally without notifying police beforehand.
Any responsible organisation will want to work within the law and to be of every possible assistance to the police.
Basil McCrea, Lagan Valley MLA
Former Ulster Unionist Basil McCrea has said that any responsible organisation will want to work within the law.
"Everybody has the right to have a parade, in the appropriate manner, there are some places where there are contentious issues that need to be resolved and we need some forum or body that's going to adjudicate in these matters," the Lagan Valley MLA said on U105.
"Whether it's the Parades Commission or some other Commission, somebody will have to say this is the right way forward, and I would expect a responsible organisation like the Orange Order, full of people who respect the law, in fact many have served within the Police, that they will comply with the law."
He said that following the example of the flag protests was "dangerous".
"The way that they (protestors) are going about it is not advancing their cause. In fact it's leading to people who might have been sympathetic to say 'no, we can't support this'," he continued.
"I don't think it helps for the Orange Order to be associated with things like that.
"It is most important that they give forward the right image for the Orange Order, the right image about Northern Ireland.
"We do not need a long summer where Northern Ireland is in the news yet again for disturbances in the street."
Alliance Justice Spokesperson Stewart Dickson says that the Orange Order are playing a dangerous game if they do go ahead with the move.
"The Orange Order should not be getting involved in this type of irresponsible behaviour," the East Antrim MLA said.
"As a community based organisation, any such move would lose them a lot of support.
"I would ask their leaders not to get involved in such actions. It would be detrimental to our society if we were to have a summer of illegal marches.
"As many of their members would be well known, I do not think they could even go through with organising parades that would be illegal."
Gerry Kelly, Sinn Féin's North Belfast MLA, said there is now "no beginning and end" to the marching season.
"We're getting it the whole year round now," the party's policing spokesperson said.
"My issue, frankly, is that we need to stop sectarian marches going past the Short Strand and indeed, Carrick Hill and Ardoyne. Now, what's the difficulty here? We're being told that there is a difficulty in the legislation."
He said the situation needed to be brought back under the control of the Parades Commission, so that the PSNI could police its determinations.
We're being told that there is a difficulty in the legislation. Well, if there's a difficulty, fix the legislation.
Gerry Kelly, Sinn Féin
Mr Kelly added that in the last few years the number of parades had increased.
The PSNI have said individuals have a right to peaceful, lawful protest but that they would act appropriately to ensure "no unnecessary disruption" is caused to the public due to demonstrations.
There have been over 180 arrests and almost 130 charges in connection with the trouble which broke out following a Belfast City Council vote in December to reduce the number of days the Union flag flies at City Hall.
On Saturday, the weekly loyalist flag demonstration will be scaled back to make way for the first official parade of the marching season in Belfast.
It will commemorate the IRA murders of two UDR soldiers in the city centre 25 years ago.
Privates James Cummings and Freddie Starrett, both 22, were killed in February 1988 when a bomb was detonated on Royal Avenue in the city centre.
A separate flags protest, which takes place every Saturday outside Belfast City Hall, has been moved to police headquarters in the east of the city. Since December, the weekly demonstrations have been held outside the historic building to protest against the decision to limit the flying of the Union flag.
A former security force colleague of the bomb victims told U105 earlier this week that the event should be used solely to remember those killed in the blast.
"I was there, caught up in the explosion, and those two young men were killed," he explained.
"I'm saying to [Jamie] Bryson and these other ones, I don't know where you're coming from, but at the end of the day, the flag protests aren't going to get you anywhere."
UUP Councillor Jim Rodgers said that he has "absolutely no doubt" the morning remembrance march into the city will pass off peacefully.
"This is a very sad occasion - especially for the former UDR men's family and friends."
He said the parade would be very dignified with five bands and around 1000 Orange men taking part.
Mr Rodgers called on all spectators to be on their best behaviour, adding that the commemoration was "not the time or place" for flag protestors.