The deputy first minister said violence that arose after Belfast City Council's move to only fly the union flag on designated days was orchestrated, on 10 December 2012.
Martin McGuinness told the Assembly both the UVF and the UDA were involved in the trouble.
He was speaking on a joint motion brought by himself and First Minister Peter Robinson on the recent unrest.
The special session, which saw the assembly begin 90 minutes earlier than normal, was supported by all five main political parties.
Mr McGuinness described the attacks on Alliance Party politicians' homes and offices as reprehensible and said they were the work of those against democracy.
He added that the death threats made towards a number of assembly members and councillors should be lifted immediately.
"I am optimistic that our message condemning the violence will be heard loud and clear beyond the walls of Parliament Buildings," he said.
Mr Robinson said the language of the motion had been carefully chosen so that it was not "controversial" but that a debate on the "flags issue" was still to come.
He said people had the right to peaceful and democratic protests, but had asked for a suspension of protests in light of the violence which had taken place.
"People have no right to attack elected representatives just because they do not share the same views," he said.
UUP leader Mike Nesbitt said he supported the motion but said people felt their Britishness was under constant attack.
SDLP leader Alasdair McDonnell said politicians needed to do more "than just condemn".
David Ford, Alliance leader, said the attacks directed towards the party were "horrific and frightening".
"An immediate priority must be to find a means to accommodate different identities through a shared approach to symbols, even if that is perceived by some, as meddling with identity," he said.
David McNarry of the UK Independence Party said the motion fell short "of expressing the full rigour of Unionist anger aimed at those who combined to take down the union flag".
The motion was passed uncontested.