Screen shots of a tweet from Jane Collins' account show a comment towards the Church Army's Mark Russell which said: "Yes because we'd soon stop your criminal activity. Paedos leave our kids alone. #Ukip."[sic]
The tweet was in response to Mr Russell's backing of a Labour candidate in the South Yorkshire police and crime commissioner by-election.
The by-election was called after the resignation of the Labour police commissioner Shaun Wright following the Rotherham child exploitation scandal.
Mr Russell immediately urged her to retract the comment. He said: "Have you heard of libel law? Apologise immediately".
But the MEP initially refused and tweeted back: "It was aimed at the paedophiles not you But South Yorkshire Police and authorities turned a blind eye crimes." [sic]
The exchange took place on 30 October
Speaking to the Guardian Mark Russell said the tweet could have damaged his work with Church Army.
He said: "I've dedicated my life to helping kids and your tweet was as hurtful as offensive ... this is my reputation.
"I merely encouraged my fellow South Yorks residents to vote for Alan Billings, the Labour candidate."
The Church Army is an evangelist charity which sometimes works with vulnerable people.
Ms Collins has now offered to make a donation to the group and tweeted: "Mark I have said it wasn't aimed at you personally and it read wrong. I unreservedly apologise for implication."
Premier has approached Ms Collins for a reply.