Unite claimed the charity was refusing to cancel plans to remove a junior staffing cap agreement and said it feared services would be harmed, because higher-paid, experienced staff were being pushed out and replaced by lower-paid junior staff.
The union said it also had issues with the charity’s "draconian" sickness and disciplinary policies.
The charity denied it was seeking to alter employee terms and conditions and that staff would be made redundant.
A statement from Unite this week said that, although 78 per cent of staff who voted opted to go on strike, one too few people who were eligible to vote had done so.
The Trade Union Act 2016 prevents a trade union from calling a strike if more than 50 per cent of employees eligible to vote did not take part.
The union, which has 500 members at Unite, said missing the minimum threshold by the narrowest margin was "hugely disappointing".
A meeting of Unite members working at St Mungo’s would take place on 18 September to "chart a way forward in the dispute with management over the erosion of employment conditions", the union said.
"The issues in the dispute that our members voted on are still unresolved," said Unite.
"Senior management have consistently refused to move on any of the matters that are of such serious and legitimate concern to the more than 500 members at this charity.
"Unite won’t be commenting further until the 18 September meeting has concluded."
Howard Sinclair, chief executive of St Mungo’s, said those who did vote for industrial action amounted to 12 per cent of all St Mungo’s staff.
"Our efforts remain focused on listening and addressing staff concerns," he said.
"Our offers to Unite remain on the table and we urge Unite officials to return to discuss these so we can build a better relationship with Unite for the future.
"St Mungo’s will continue to do everything necessary to protect the safety and interests of our most vulnerable clients."