Pamela Nash, chief executive of Scotland in Union (SiU), called for the commission to be given the appropriate amount of time and resources to carry out a thorough assessment.
Her letter to Nicola Sturgeon was prompted by comments made by Penny Curtis, deputy director at the Scottish Government, who told a Holyrood committee last month that legislation would allow ministers to stick with the straight Yes/No question which was used in 2014.
Curtis insisted that the aim was to avoid confusion among voters.
In her letter to the SNP leader, the SiU boss said: “Since 2014, we have experienced the referendum on the UK’s membership of the European Union, prior to which the Electoral Commission was asked to assess the proposed referendum question. It recommended that a Yes/No question should not be used.
“The Remain/Leave question was adopted as it was both easier to understand and more balanced. The Electoral Commission has said that this change from the advice it gave in October 2013 was the result of having more time to examine further evidence.
“The overwhelming majority of people in Scotland do not want a second referendum within the proposed two-year time frame that you recently put forward.
“However, I understand that you are likely nonetheless to push ahead with your stated aim of securing another such referendum. In the event that such a referendum was to be agreed with the UK government, it is vital that it would be carried out fairly and the result would be respected by all.
“Therefore, can you please confirm that your Government will seek the advice of the Electoral Commission on the wording of the question?”
Ministers unveiled a bill in May which lays the foundations for a future plebiscite north of the border, with MSPs to be given a vote on the legislation by the end of the year.
Constitutional affairs spokesman Mike Russell told MSPs it would be for them to vote on the proposals and on any regulations made under them.
Responding to the letter from SiU, a spokesman for Russell said: “These suggestions are incorrect – the Bill makes specific provision for the involvement of the Electoral Commission to consider the proposed referendum question.
“But it is welcome that Scotland in Union now seem to recognise that an independence referendum is now going to take place.”