The motion to sign up to a UK-wide crime taskforce, described as the UK's "FBI", was debated in Stormont on Monday, but did not get the backing needed to go ahead.
The SDLP and Sinn Féin blocked the plan because they want policing powers to be retained within the region.
Justice Minister David Ford said during the debate that there would have been concessions so that power of policing remained in the region's control.
But Sinn Féin MLA Pat Sheehan warned that the national body would lead to a "two-tier" model of policing in Northern Ireland, which he claimed would not have the same level of accountability.
"Unaccountability was the poison at the heart of policing in the past," the west Belfast representative said.
"The Patton proposals recognised that and made allowance for the setting up of the Policing Board and the Police Ombudsman office, oversight and accountability mechanisms."
Mr Sheehan said that his party would potentially support the taskforce if legislation was amended and added that there should be greater cooperation between police agencies across the UK and Ireland.
SDLP MLA Conall McDevitt said the key sticking point in the debate was accountability of any National Crime Agency officers.
Ulster Unionist MLA Tom Elliott claimed that the model would be more accountable than its predecessor, the Serious Organised Crime Agency.
"This is about international crime, about drug trafficking, people trafficking, paedophilia, internet scams," he said.
We are committed to delivering a UK-wide crime fighting agency focused on tackling serious, organised and complex crime, and are now looking carefully at the provisions to see how they can best be modified to mitigate operational impact.
Home Office statement
Speaking after a meeting with the Director General of the National Crime Agency, Mr Elliott criticised Sinn Féin and the SDLP's refusal to support the move.
"The benefits of having the NCA operate in Northern Ireland include law enforcement here being able to access skills at a National UK level, and take advantage of economies of scale," the Fermanagh and South Tyrone MLA said.
"It is quite staggering that anyone could support measures which will diminish our capacity to tackle organised crime including cyber-crime, economic crime, drug gangs and child exploitation.
"The safety of our citizens must be paramount and the SDLP and Sinn Féin must explain why they want to bring about a situation whereby Northern Ireland is the weak link in the UK's fight against organised crime."
DUP Lagan Valley MLA Paul Givan said nationalist parties had already signed up to the system in principle.
"Nationalists signed up to the devolution of Policing and Justice which included SOCA operating on a UK-wide basis and in which MI5 not just operates, but has a vital base in Northern Ireland," he said.
"It is time that nationalist representatives left this politically and morally bankrupt competition behind and actually worked with the NCA."
North Antrim DUP MP Ian Paisley added: "This has nothing to do with devolution given that organisations such as SOCA have already operated in Northern Ireland on a similar basis."
It is thought that organised crime costs the UK up to £40bn a year and in Northern Ireland there are particular problems with illegal fuel laundering as well as international people and drugs trafficking.
Alliance Justice spokesperson Stewart Dickson MLA said not implementing a National Crime Agency in NI would make it harder for police to deal with organised crime.
"The alternative to the NCA operating in Northern Ireland is a bigger burden on an already overstretched PSNI," he said.
"It will fragment efforts to tackle crime nationally and internationally and, quite frankly, make us a laughing stock across the border and throughout Europe."
"Organised crime is increasingly trans-national, with no respect for borders, and crime groups are quick to take advantage of
Labour Shadow Secretary for Northern Ireland, Vernon Coaker MP said it was "imperative that the NCA has the ability to fight organised crime right across the UK".
"Northern Ireland is the only part of the UK that has a land border, and so the NCA has a particularly important job to do in combating serious crimes like trafficking and smuggling," he said.