The question will now be whether people wish to remain in or leave the EU after Prime Minister David Cameron accepted the Electoral Commission's advice.
It had said asking a yes/no question in the vote, promised by the end of 2017, could create a possible bias.
An amendment to be tabled by the Government when the Bill returns to Parliament on September 7 will propose changing the question to: "Should the United Kingdom remain a member of the European Union or leave the European Union?"
The responses would be "Remain a member of the European Union" or "Leave the European Union".
Christian Ukip MEP Jonathan Arnott welcomed the move: "To me that's a simple question of fairness. It seems to me that if you have a choice to go from a leading question to one which is not leading, it's much better to have the one which is not leading.
"So it's good to see that the Electoral Commission, for once at least, has got something right and that the government's going to go ahead with it".
Electoral Commission chair Jenny Watson said: "Any referendum question must be as clear as possible so that voters understand the important choice they are being asked to make. We have tested the proposed question with voters and received views from potential campaigners, academics and plain language experts.
"Whilst voters understood the question in the bill some campaigners and members of the public feel the wording is not balanced and there was a perception of bias. The alternative question we have recommended addresses this.
"It is now for Parliament to discuss our advice and decide which question wording should be used."
The Prime Minister's official spokeswoman said: "We will accept the Electoral Commission's recommendation and we will table an amendment to the bill accordingly."