The vote was taken under an emergency motion put forward at last night’s Bolton West Constituency Labour Party (CLP) with 50 to 19 voting in favour.
Cllr Morris said he was ‘disappointed’ by the move and said he had asked for it to be deferred so he could attend the meeting.
The vote comes just days after Frank White was removed as chairman of the Bolton Labour Party with party secretary Sheila Jones.
It is understood the motion was put forward by Ms Jones.
They are understood to have questioned the suitability of Cllr Ismail Ibrahim, who was exposed last year for not paying his council tax on time.
He failed a Labour interview to be reselected as a potential candidate – but successfully appealed with the support of Cllr Morris.
A Bolton Labour Party source said: “It is pretty bad, I have never known a CLP to put a vote of no confidence in the leader before. In terms of reputation, it has been damaged.
“It sends a message to him that saying they are not happy.
“This motion was the repercussion and reaction of what has happened.”
The vote was described by others at the meeting as a ‘landslide’ and dramatically showed that support for Cllr Morris had been withdrawn.
A vote of no confidence has no practical implication for Cllr Morris.
The CLP does not have the power to remove him. Only the Labour Group has that power.
Cllr Morris said: “I am disappointed in the motion and discussion at Bolton West last night.
“Some of the issues discussed related to decisions made by a fair and transparent Labour Party process.
Unfortunately, a few individuals, who are unhappy with the outcome, have used the motion to re-run this process.
“As for the discussion about my leadership, I had asked for this to be deferred to a future meeting when I could attend as I was already committed to be present at the Bolton and Bury Business Awards last night. This would have have been a simple courtesy to allow proper discussion.
“My leadership is a matter for my group, not the wider Labour Party.
“Although we have had some difficult issues to face in recent times – and some great successes – I have always been fortunate to have the support of my group for my leadership and direction.
“Challenges such as this are a normal part of political life, as can sometimes been seen locally and nationally.”
Another person who was at the meeting said it would make Cllr Morris' situation 'difficult' and not do his public perception 'any good' — but added: "He should have been given the opportunity to talk, had this been done in an employment situation, it would go against Labour Party principles if the person did not have the opportunity to put their side forward."
Tory leader Cllr David Greenhalgh said: "It's one thing being criticised by your political opponents, but when your own local Labour party members have lost faith in you, and take the drastic and damaging decision to humiliate you publicly by passing a vote of no confidence in you, then I really don't see why Cllr Morris would even want to try to hang on as Leader. It's time to go!
"I would imagine there will be some interesting meetings taking place among the different factions within the Labour Group, which up till now has given their full backing to Cllr Morris on every decision he has been challenged on, including more recently the Asons debacle."
He added: "These Labour Party members, who passed the vote of no confidence, are the same members who will be selecting candidates for the local elections in May. They also have powers to de-select sitting councillors.
"I would imagine there may be some nervous Labour Councillors around if they have not already secured their re-selection.
"Clearly Labour locally is utterly divided, but no matter whatever issues opposition parties highlight or raise, whatever the public think or call for Cllr Morris's resignation, if he doesn't go of his own accord, only those Labour Councillors in the Labour Group can get rid of him as Leader of Bolton Council. Interesting days ahead, I think."