Just days away from contesting a parliamentary by-election in Stoke-on-Trent, Mr Nuttall is now facing calls to resign as an MEP and was branded a "coward" after a party press officer offered to take the blame over the posts.
Mr Nuttall has apologised over the claim, carried on his official website for at least six years, after he was forced to admit it was wrong during a live radio interview.
Today a message on paulnuttallmep.com said the site was offline for "scheduled maintenance".
Paul Nuttall's website was taken down amid Hillsborough disaster false claims row
Paul Nuttall is a coward. You cannot believe a word that comes out of his mouth
Tim Farron, Liberal Democrat leader
Liverpool Mayor Joe Anderson has called on the Ukip leader to "explain himself to the people of Liverpool".
He said: "It's not the press officer who should be offering their resignation, it should be Paul Nuttall offering his resignation as a candidate, never mind for what party."
Meanwhile Liberal Democrat leader Tim Farron branded Mr Nuttall a "disgrace", adding: "Paul Nuttall is a coward. You cannot believe a word that comes out of his mouth.
The website falsely claimed Nuttall had lost loved ones in the Hillsborough disaster
"And every time he gets caught making things up, he just blames it on the office junior. The man is a disgrace."
Mr Nuttall has stood by his account that he was at the stadium when tragedy struck on April 15 1989.
However families of some of the 96 Liverpool fans who died in the disaster have voiced their anger at the false claim that he lost close personal friends.
Get Quotes on Home Insurance
Barry Devonside, whose son Christopher, 18, was among the victims, said the Ukip leader's credibility had "gone out of the window" and branded the post "insensitive".
Liverpool Mayor Joe Anderson has called on the Ukip leader to 'explain himself to the people'
Lib Dem leader Tim Farron has called Nuttall 'a coward'
"We don't need this kind of thing from Paul Nuttall. He should know better as a politician and leader of Ukip," Mr Devonside said.
Hillsborough Family Support Group chairwoman Margaret Aspinall told LBC radio: "A lot of people who were there that day did lose close personal friends and I think it's an insult to them as well as to all the families who did lose somebody on that day."
Mr Nuttall apologised on Tuesday for the claim – contained in at least two press releases on his website – after being challenged during an interview with Radio City Talk in Liverpool.
He told presenter Dave Easton: "I haven't lost a close personal friend, I've lost someone who I know. I haven't put that out, that is wrong."
Hillsborough 25 years on
Tue, April 15, 2014
The memorial service marking the 25th anniversary of the Hillsborough disaster
1 of 10
MP Andy Burnham takes his seat after his speach, during the Hillsborough 25th Anniversary Memorial Service at Anfield Stadium, Liverpool
On Tuesday Ukip press officer Lynda Roughley said she was "entirely responsible" for the website post and had offered her resignation.
A Ukip spokesman said on Wednesday that the resignation had been rejected, adding: "Obviously Paul is grateful for her offer, but what sort of chap would he be to say her career is dead for what seems to be a minor error six years ago?"
In a statement Mr Nuttall made clear he stands by his account of being present at the disaster as a 12-year-old fan, after doubts were raised by the Guardian.
"From the upper tier of the Leppings Lane end of the Hillsborough Stadium, I watched the events of that day unfold with horror," he said.