Mr Malik says he has been the victim of religious hate crimes
A government minister has warned that many British Muslims "feel like the Jews of Europe".
Dewsbury MP Shahid Malik, who is a minister for international development, stressed that he was not equating the Muslims' situation with the Holocaust.
But, in an interview to mark the 7 July bombings anniversary, he suggested that many Muslims felt "under siege".
This had the effect of segregating society and undermining efforts to deal with extremism and terrorism, he said.
Mr Malik, who revealed he had been the victim of religious hatred himself, made the comments in an interview for a Channel 4 Dispatches programme.
He said: "I think most people would agree that if you ask Muslims today what do they feel like, they feel like the Jews of Europe.
"I don't mean to equate that with the Holocaust but in the way that it was legitimate almost - and still is in some parts - to target Jews, many Muslims would say that we feel the exact same way.
"Somehow there's a message out there that it's OK to target people as long as it's Muslims.
"And you don't have to worry about the facts, and people will turn a blind eye."
David Brown, from the Jewish Life Education Centre, said he did see some parallels between the persecution of Jews in the 20th Century and the contemporary treatment of Muslims.
"If you think about the earlier stages of what was going on in Europe in the later (19)20s and early (19)30s and the way that Jews were scapegoated and stereotyped, I can certainly understand a sentiment of that is going on for the Muslim community," he said.
The documentary - which investigates whether the fear of terrorism has fuelled a rise of violence, intolerance and hatred against British Muslims - will be broadcast on Monday to coincide with the third anniversary of the 7 July London bombings.
British society is in danger of becoming segregated, Mr Malik said
Mr Malik's constituency in West Yorkshire was home to 7 July suicide bomber Mohammad Siddique Khan.
The MP, who told how his car was firebombed, a car drove at him in a petrol station and said he receives regular hate mail, called for action to be taken to help Muslims feel accepted in society.
"It is critical we ensure that Britain's near two million Muslims have a sense of belonging and feel accepted, first and foremost because it is their right as British citizens, but secondly because it is vital in the fight against violent extremism in the name of Islam," he said.
"With some 2,000 people under surveillance because of the possibility that they might engage in terrorism the threat of an attack is a very real one and Muslims in communities up and down the country become indispensable in the fight against terrorism.
"Yet there is no doubt that many Muslims feel under siege in the media and in society and this siege mentality feeds into a wider victim narrative."
Mr Malik said the apparent persecution made it more difficult for people in positions of responsibility to persuade people to challenge the "small minority of extremists who call themselves Muslims".