Flanagan was a social conservative, who famously claimed that "there was no sex in Ireland before television".[4] An anti-semite and anti-Mason, he used his maiden speech in the Dáil, on 9 July 1943, to urge the government to emulate the Nazis and "rout the Jews out of this country... where the bees are there is honey, and where the Jews are there is money" and called for the banning of the Freemasons.[5]
Nonetheless, he was consistently popular in his own constituency, largely because of the attention he paid to individual voters' petitions and concerns. He has been described as "one of the cutest of cute hoors in the history of the Dáil".[6]
Flanagan first held political office in 1942, when he was elected as a Councillor to Laois County Council, a position he would hold for almost forty-five years.
During the campaign, Flanagan wrote to Fr Denis Fahey: "Just a line letting you know we are going ahead with the election campaign in Laois-Offaly against the Jew-Masonic System which is imposed on us. The people are coming to us – but it's hard to get the people to understand how they are held down by the Jews and Masons, who control their very lives."[9]
He used his maiden speech in the Dáil to urge the government to use the Emergency Powers Acts to "rout the Jews out of this country":
How is it that we do not see any of these Acts directed against the Jews, who crucified Our Saviour nineteen hundred years ago, and who are crucifying us every day in the week? How is it that we do not see them directed against the Masonic Order? How is it that the I.R.A. is considered an illegal organisation while the Masonic Order is not considered an illegal organisation? [...] There is one thing that Germany did, and that was to rout the Jews out of their country. Until we rout the Jews out of this country it does not matter a hair's breadth what orders you make. Where the bees are there is the honey, and where the Jews are there is the money.
During a 1952 Dáil debate, after John A. Costello had said "I made no reference to an Adoption of Children Bill", Flanagan quipped "Deputy Flynn would be more qualified to do that".[11]John Flynn, who was not in the chamber at the time, interpreted this as an insulting innuendo, and later punched Flanagan in the Dáil restaurant.[12] The Dáil Committee on Procedure and Privilege condemned the conduct of both TDs.[12]