The assessment, to be published in mid-October, will be used to inform parties at Northern Ireland's political talks.
In a statement on Friday, Northern Ireland Secretary Theresa Villiers said she is also to establish a fund to tackle organised crime associated with paramilitary groups.
The two unionist parties now say they will join cross-party talks on Monday.
Unionists had said the issue of continued paramilitary activity was crucial to their involvement.
Democratic Unionist Party leader Peter Robinson said he was "content" with the announcement.
"Policing and security in Northern Ireland is not just the responsibility of the Northern Ireland Executive, the secretary of state has a particular responsibility as well," Mr Robinson said.
The National Crime Agency (NCA) became operational in Northern Ireland in May.
Given its wide-ranging remit and resources, it would be reasonable to assume it knows the extent of paramilitary involvement in organised crime in Northern Ireland.
It should be in a position to provide an assessment of paramilitary involvement to the Northern Ireland Secretary and political parties.
So, it seems unlikely that the review to be published by the independent panel in October will tell Theresa Villiers and political parties anything they could not be told today by the NCA and the Police Service of Northern Ireland.
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He said "permanent and statutory steps" to address paramilitary activity and links should be determined within the talks process.
The Ulster Unionist Party leader Mike Nesbitt described Ms Villiers statement as a "positive step forward".
Ms Villiers said the assessment of paramilitaries would be carried out by UK security agencies and the Police Service of Northern Ireland, and would be reviewed and checked by three people whose names would be announced early next week.
"I also intend to establish dedicated funding aimed at increasing the capability of agencies working to tackle criminality and organised crime associated with paramilitary groups in Northern Ireland," she said.
"It will support agencies to enhance specialist capabilities such as forensic accounting to strengthen their capacity to seize criminal assets.
"Lastly, I am planning to discuss with the Northern Ireland justice minister and the Irish justice minister how we can work best together in our efforts to tackle cross-border crime."
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In response, Sinn FÃ©in's Martin McGuinness said: "Obviously with today's developments and the response of unionist leaders, as we hoped all-party talks will resume on Monday.
"We're entering the talks on Monday in a positive and constructive spirit."
But on the subject of the assessment, the deputy first minister added: "I don't think anybody is going to learn anything over the next four weeks that they didn't know over the last 20 years."
The Police Service of Northern Ireland's Chief Constable George Hamilton said he welcomed the "clear focus" on organised crime that the assessment would provide.
Irish Foreign Minister Charlie Flanagan said it would be a "once-off exercise".
He added that it was intended to assist the political parties in considering "how the impact and legacy of paramilitary activity should best be addressed".
Alliance Party leader David Ford said the assessment was a positive move but added: "This may serve a range of purposes but we remain committed to exploring a standing mechanism."
Alasdair McDonnell, the leader of the SDLP, said what was needed was more than just a briefing "but a real sense that all paramilitary structures including financial, intelligence and military are disbanded and that illicit cash flows and assets are accounted".
Traditional Unionist Voice leader Jim Allister said Ms Villiers' statement "has all the appearance of politically motivated and timed window-dressing to keep the failed process going".
The government has commissioned an independent assessment of paramilitary organisations in Northern Ireland.