The Labour MP who questioned the loyalty of the UK's first Jewish ambassador to Israel has apologised for his remarks. At the same time, the Green Party issued an apology on behalf of its deputy leader in Wales for similar comments she made.

In a letter to the JC on Wednesday, Paul Flynn, MP for Newport West, accepted that his "clumsily expressed remarks" had caused anger and upset.

"I greatly regret the interpretation that has been placed on them and I fully understand why offence was given," he said. "Some of the interpretations of these words were exaggerated suggesting malign intent that was never present or intended."

Mr Flynn had told the Public Administration Select Committee of his concerns that Matthew Gould, who took up the post last year, "has proclaimed himself to be a Zionist".

Challenged by the JC to explain his remarks, Mr Flynn claimed that previous ambassadors to Israel had not been Jewish "to avoid the accusation that they have gone native". His comment that Britain needed "someone with roots in the UK [who] can't be accused of having Jewish loyalty" caused outrage across the political spectrum.

The veteran MP initially stood by his remarks, last week describing the idea that his remark could in any way be seen as antisemitic as "ludicrous".

But on Monday afternoon he was called in to see Opposition Chief Whip Rosie Winterton, who told him that his comments would not be tolerated within the Labour Party. The JC understands Ed Milband's office also intervened to put pressure on Mr Flynn.

A Labour source said: "The Chief Whip has spoken to Paul Flynn. He has recognised that his remarks were unacceptable. He has withdrawn them and apologised."

The comments had originally been challenged by Mr Flynn's fellow committee member Robert Halfon, the MP for Harlow. He said he now recognised that Mr Halfon's criticism was fair.

"Other greatly respected friends have urged me to withdraw the remarks and apologise. This I am happy to do.

"There is no reason that anyone of any race or religion should be debarred from public office. That has always been my opinion. The comments were made in a heated exchange in a select committee discussion on probable warmongering. Other information [I have] received contradicts criticism I quoted on the conduct of our ambassador. I regret any offence caused."

Mr Flynn said his original intervention had been motivated by a desire to alert people to the danger of being drawn into a war in Iran. Media speculation had suggested that Dr Fox, Mr Werritty and Mr Gould had discussed military intervention in Iran.

Mr Halfon said: "Paul Flynn is a decent man and I think his apology shows this. I hope it stops this kind of talk, not just from him, but others on the left in future."

Jennifer Gerber, director of Labour Friends of Israel, said: "LFI is pleased that Paul Flynn rightly apologised for the remarks. We made clear from the start that what he said was completely unacceptable."

After issuing his apology, Mr Flynn then told the JC that he would be making an entry on his blog with the headline: "How I became Hitler".

Meanwhile, the Green Party apologised for remarks about Jewish diplomats in Israel made by Pippa Bartolotti, deputy leader of the Greens in Wales.

As one of Mr Flynn's constituents, it was Ms Bartolotti who first brought the allegations about the British ambassador to Mr Flynn's attention.

Last July she was arrested as part of the "flytilla" protests in Israel. Ms Bartolotti told the JC last week: "I questioned the wisdom of having a Jewish Zionist ambassador in Israel and stated that their loyalty was a matter for the FCO to investigate." She added: "The vice -consul was called Levi. From the university of life I have learned that Jews often have a conflict of interest in matters relating to Palestine."

A statement issued by the Green Party on Wednesday stated: "Pippa Bartolotti has apologised for any offence which her comments may have inadvertently caused. Needless to say, the Green Party does not condone antisemitism in any form, and we regret if any other impression were given on this occasion."