The union has had a voluntary recognition agreement with the charity since 2005, meaning that it can officially represent Samaritans staff in disputes and pay negotiations.
Unite claimed that, at a recent meeting to renew the agreement, Samaritans reneged on the agreement and has since refused to discuss the matter.
The union said it will now try to trigger a "statutory recognition process" that would require the charity to recognise the union.
Unite declined to confirm how many members it has at the charity, which employs 110 people, but said it has the minimum of 21 members needed to trigger the recognition process.
"Samaritans, the charity that has helped people with their problems for 60 years, has a problem of its own," Unite said in a statement. "It has derecognised Unite as the union representing its staff."
But a statement from Samaritans said this was not accurate and that the charity was keen to put in place a new voluntary recognition agreement that "accurately reflects the needs of the organisation in the context of the number of staff that are members of the union".
Samaritans said it believed there to be "quite low" numbers of union members on its staff.
"We are very disappointed that Unite has today announced that Samaritans has ‘derecognised the union’," the statement said. "It is surprising that this statement has been issued as it is our impression that we have been working with Unite."
Jamie Major, regional officer at Unite, said Samaritans was refusing to meet him and that he therefore assumed the charity was no longer interested in putting an agreement in place.
He said Unite members had been told they were not entitled to train as union representatives because Unite did not officially represent them.
"As management no longer recognises our agreement, we have no other option but to consult our members working at Samaritans about the action they are prepared to take in response," he said. "Industrial action will obviously be one of the options we will be discussing, if management refuses to negotiate."