However former Army officer Mr Bolton, who was honoured by the Queen for his military record, last night said he would fight on, forcing the party to put his fate in the hands of Ukip's 24,000 members at an extraordinary general meeting next month.
"The party is required to hold such an EGM within 28 days of today's date unless Henry Bolton resigns in the meantime".
Should he lose the vote of confidence among the membership, the resulting leadership election could well bankrupt the the party.
A statement from the party chairman, Paul Oakden, said the NEC heard a statement from Bolton, after which members "asked a number of questions pertaining to that coverage".
UKIP'S leader Henry Bolton has insisted he will not quit and has admitted that the party "is probably over" if he is forced out as he prepares to face down critics at a meeting of its ruling body today.
The decision by Ukip's National Executive Committee would seemingly bring down the curtain on Mr Bolton's four month reign as Ukip leader which has unravelled spectacularly since his relationship with Jo Marney emerged last month.
Mr Bolton, 54, told ITV's Peston On Sunday the party could not afford to have another leadership contest.
Paul Oaken said Henry Bolton recognises the "strength of feeling in the NEC but "equally he feels as though he is the right man to take the party forward".
A well-placed source said a fresh leadership election to replace the under-fire Bolton could cost between £30,000 and £60,000, and it might need to axe staff in order to finance the contest. The vote was carried unanimously with the exception of the leader.
Buttler's ton helps England lock series against Aussies
Meanwhile, Eoin Morgan believes England's performance in the third ODI has shown his side are peaking towards the 2019 World Cup. He then took a contentious catch to dismiss Steven Smith at a key point in the chase as England held on to go 3-0 up.
However, allies of Mr Farage believe that he could join a party dubbed "Ukip 2.0" if Mr Bolton was removed from his position.
"This decision will automatically trigger an emergency general meeting of the party, to allow the membership of Ukip the democratic opportunity to decide to endorse or reject that vote of no confidence".
Despite claiming to have ended his relationship with model Jo Marney, the pair have continued to be seen together both in a London restaurant and travelling on a train to Folkestone, where Mr Bolton has a flat. My own personal life, it's a little bit of a mess at the moment.
Members will be told about when and where it will be held in the next 10 days. "We have spoken a couple of times on the phone, but that is my business".
Neil Hamilton, Ukip's leader in Wales, said Mr Bolton should "seek psychological help".
Mr Bolton is the latest in a string of people to be elected leader of Ukip.
"He should now resign from Ukip immediately so we can get on with rebuilding the party without further distraction".
Bolton's was the only vote in favour of his staying in the role after an emergency meeting to consider the fallout from his relationship with a much younger party activist who was found to have sent racist text and social media messages. He said: "His recent behaviour has been so irrational, he should seek psychological help".