It comes as polls suggest UKIP's share of the vote in the European elections, whose results will be announced on Sunday, could be as low as three per cent, with Nigel Farage's Brexit Party in the lead by some margin, at 32 per cent.
In a letter sent to officials at the close of polls the Hull-based MEP said he believed "UKIP always has been and always should be, a libertarian party" with "broad electoral appeal".
But he added; "However, under your leadership, and despite my appeals, UKIP has been derailed from this objective.
"Your policy direction and associations have given the mainstream media the ammunition to label our party “extreme” and “far-right”; accusations I do not believe to be true."
Mr Batten has already said he will stand down on June 2, launching a leadership contest.
He has been UKIP leader for 16 months and appointed former English Defence League leader Tommy Robinson as his political adviser in November 2018.
Revealing his growing frustration, Mr Hookem said: "I have been desperate to act to stop the increasing isolation and marginalisation of our party in recent months.
"However unlike some who found alternative parties, I stayed loyal to the membership and delayed my resignation to minimise any potential electoral impact.
"I also wanted to make sure my resignation was unconditional on the outcome of yesterday's European elections."
Mr Hookem, an MEP who stood for re-election this week, said Brexit had been a "golden opportunity for Ukip", which was led by Nigel Farage before he stepped down in 2016.
He said Mr Batten had "squandered our natural advantage and seriously undermined 26 years of work in the process".
Asked what would happen is he was not re-elected he said: "If I'm not MEP that's what people want but I will carry on fighting for the party that I loved and joined over 20 years ago.
"I will go for the leadership as I believe there's a place for UKIP in politics."