On Monday SNP leader Nicola Sturgeon told Glasgow’s Jewish community that it was not acceptable to use the Israeli-Palestinian conflict to justify attacks on Jews.
Dr Monaghan entered Parliament in May as the SNP took 56 of the 59 constituencies in Scotland.
The JC understands his past comments were already a cause for concern among campaigners working to tackle antisemitism in politics.
During Israel’s Operation Pillar of Defence in late 2012 – in response to Hamas rocket attacks from Gaza – Dr Monaghan tweeted: “Sad to see the proud Jewish race, so ashamedly persecuted by the Nazis, now persecuting the people of #Gaza. Are memories so short?”
He posted the message again a day later, changing the wording to read that “proud Jewish people” had been “hideously persecuted”.
In a statement to the JC on Wednesday Dr Monaghan said: “I share the commitment set out earlier this week by the First Minister to the Jewish community.
“I am sorry for my comments, they were certainly not intended to cause offence and I have removed them to ensure no further upset is caused.”
The SNP has not yet commented on the remarks.
At the time the posts had been tweeted Dr Monaghan was a director of a homelessness charity. He joined the SNP more than 20 years ago and was selected in January to stand for the Caithness, Sutherland and Easter Ross seat at the general election.
His Twitter remarks were similar to those of controversial former Liberal Democrat MP David Ward , who accused “the Jews” of “inflicting atrocities” on Palestinians ahead of Holocaust Memorial Day in 2013.
On Monday, Scottish First Minister Nicola Sturgeon spoke at Glasgow's Giffnock and Newlands Synagogue complex to reassure the Jewish community about her party’s intention to challenge antisemitism.
Ms Sturgeon told the JC that whatever “the rights and wrongs of the Israel-Palestine situation", it should never be used "as some kind of justification for attacks on Jewish people, or abuse towards Jewish people, or Jewish people in any way being made to feel responsible for the actions people are disagreeing with. That's a point that has to be made at every level of Scottish society very, very strongly”.
Danny Stone, director of the Parliamentary Committee Against Antisemitism Foundation, said: “The 2015 All-Party Inquiry into Antisemitism report addressed in detail concerns about antisemitic discourse and the responsibility of public figures to set the right tone for our national debate.
“We are continuing to work with all parties to deepen understanding about antisemitism and do hope Dr Monaghan, and indeed MPs of all parties, will avail themselves of the various briefing opportunities they have been offered through the All-Party Parliamentary Group”.
Dr Monaghan had previously also claimed on Twitter in 2013 that Westminster had become “absolutely repugnant – increasingly feels like early days of the Third Reich”.
Last year he posted a message to an SNP supporter which stated: “What the ‘British’ did to the people of India beggars belief. Easily on a par with Nazi atrocities.”
In April last year he said Israel was embarking “on genocide”.
Earlier this year the Dr Monaghan was criticised for appearing to encourage a racist SNP supporter who had posted offensive tweets on the social media site.
A constituent of Dr Monaghan told the JC this week: “I take antisemitism very seriously and I am dismayed that my MP has written these tweets, some of which are certainly antisemitic in tone and effectively belittle the Holocaust and the Third Reich.”
