Seven searches were carried out on Tuesday under the Terrorism Act by the PSNI with support from HMRC officers.
Two assault rifles and one submachine gun have been seized.
As well as the weapons, a quantity of Class B drugs, counterfeit clothing and DVDs, around £13,000 in cash, phones, tablets, documents, more than 7,000 illicit cigarettes and a quantity of hand-rolling tobacco were seized.
Two men, aged 44 and 43, have been arrested and are in police custody assisting officers with their enquiries.
A further search was carried out in relation to the investigation in Derry area led by HMRC and supported by PSNI.
An Garda Siochana carried out a search in Co Donegal in which around 60,000 illicit cigarettes, a large quantity of tobacco, a large quantity of counterfeit clothing, DVDs and other items including money were seized during the operation.
District Commander, Superintendent Gordon McCalmont said: “The INLA in Londonderry and Strabane claim to be the protectors of their community, but the reality is that they use violence and intimidation to control and exploit those communities.
“Weapons like the ones seized today pose a threat to everyone and anyone who brings guns onto our streets does not care about our community.
“When a gun is fired there is no guarantee where the bullet could end up or who it could harm and the people of our city have seen the damage and devastation that this can cause.”
“Despite what they say, it is clear that they do not mind drug dealers operating in the local area– as long as they’re getting their ‘cut’ from the profits,” the senior officer said.
“The INLA are hypocrites allowing those supplying illegal drugs to continue ruining the lives of those with addiction so long as they pay up.
“And if they don’t they are threatened with severe violence and murder. Local families suffer at the expense of INLA members lining their pockets.
“Furthermore, the INLA are heavily involved in the supply of counterfeit goods and illicit cigarettes and whilst the supply of these items may seem like victimless crimes, profits made from the sale of these items can help to fund INLA terrorism and criminality which brings misery and harm to the local community
“Through working closely with HMRC, An Garda Siochana and other partners, we will continue to tackle Paramilitarism. We know that the communities most affected by these groups support our ongoing efforts.
“I would appeal for anyone with information regarding criminality by paramilitary organisations to contact police on 101.“Alternatively, information can also be provided to the independent charity Crimestoppers on 0800 555 111 which is 100% anonymous and gives people the power to speak up and stop crime.”
Steve Tracey, Assistant Director, Fraud Investigation Service, HMRC, said: “Working together in partnership with other enforcement colleagues we can target the criminal gangs who are stealing from the taxpayer, robbing public services and undermining legitimate traders.”