While the factors behind the unrest were “complex”, he conceded that they included tensions around the NI protocol, negotiated by Boris Johnson’s government as part of his Brexit divorce deal with the EU.
But he faced anger from DUP MPs who told him the protocol was the root cause of the disorder and was “disrupting peace”.
Anticipating criticism from opposition politicians on the issue, Mr Lewis had earlier told MPs: "It can be easy to look for a simplistic explanation for the recent disorder, however it is clear that the factors behind it are in fact... multi-faceted."
These included fears coronavirus restrictions were not being applied equally in Northern Ireland, following the presence of high-profile Sinn Fein politicians at a controversial republican funeral, he suggested.
But in a comment directed at Brussels, Mr Lewis also called on the UK’s “friends and partners” in the EU to “fully understand” the importance of identity to Northern Ireland’s loyalists.
It is within the loyalist community where concerns over the NI protocol, and the border down the Irish Sea it has created, have bubbled over in recent weeks.
Shadow Northern Ireland secretary Louise Haigh called on Mr Johnson, who led the Brexit campaign which critics warned would lead to an internal border within the UK and potentially rock the fragile peace in Northern Ireland, to “face up to the consequences of his own actions and show the leadership communities are crying out for”.
She said: “Northern Ireland has been relegated to little more than an afterthought and the promise of peace allowed to stall.
“It demands that the vacuum of leadership and strategy that Northern Ireland needs is now filled. The Prime Minister must face up to the consequences of his own actions and show the leadership communities are crying out for.”
She too said the violence was “unjustified and unjustifiable”, adding: “Recent months have shown just how fragile the peace is and that it requires responsible and careful leadership to safeguard.”
Mr Lewis defended the prime minister, insisting that he had been “involved in this all the way through”.
But he came under fire from his party’s former partners in government, Northern Ireland’s DUP.
DUP MP Ian Paisley Jnr said the funeral was not the cause of the unrest but rather the “straw that broke the camel’s back”. The real cause was the NI protocol which meant the “identity of Ulster was at stake,” he said.
DUP MP Jim Shannon said the NI protocol had “disrupted business and created disorder on the streets” and was “disrupting peace”.
SDLP leader Colum Eastwood also accused the UK Government of failing to be “honest” with the loyalist population about the consequences of Brexit.