The official Find Madeleine Campaign group, endorsed by the McCanns, said it has experienced a spike in abuse over the past few weeks.
It's claimed the spike came after Kerry Needham, whose own son Ben vanished 24 years ago in Greece, questioned the huge sum of police money spent on the search for missing Madeleine McCann.
A statement from the Find Madeleine Campaign said: "After talking with Kate and Gerry yesterday, we have decided to delete our Twitter account and focus on Facebook.
"They agree it's time to remove ourselves from a place that allows so much toxic content to be directed at us and does not permit us the ability to protect ourselves from people who want to damage the search for Madeleine.
"I have been dismayed, however, at some of the hatred and sheer viciousness directed at Kate and Gerry through our social media accounts for no logical reason at all.
"At times, it has had me in tears. It is hard to accept that some people can be so cruel to a family that has already experienced the worst pain imaginable."
Tension has been building between the two missing persons campaigns in recent weeks, and Kerry Needham has criticised the decision to shut the social media account.
Ms Needham told the Daily Mirror: "It feels like a personal attack on me. It is deeply, deeply hurtful.
"I have myself had massive amounts of slanderous abuse from supporters of the McCann campaign in the past but I have never taken that personally
"I have never criticised the McCann family. I have only ever criticised the authorities for the way the two cases have been handled so differently."
McCann family spokesman Clarence Mitchell said: "Kate and Gerry McCann have always supported the Find Ben Needham campaign, indeed they have promoted it on their own Find Madeleine social media platforms.
"There is no spat between the two campaigns.
"Because of continued and ill-informed abusive comments by some social media users a decision has been taken to close down the Find Madeleine Twitter account.
"Kate and Gerry continue to wish Kerry Needham the best for the future and hope she will one day be reunited with Ben, as they too hope similarly to be reunited with Madeleine."
Three-year-old Madeleine disappeared back in May 2007 while on a family holiday in Praia da Luz, Portugal.
The McCanns, who are Catholic, have often credited their faith for getting them through the difficult time since she went missing.