People who complete the next Scottish census should be advised to fill in the male/female question based on how they identify themselves rather than according to any legal status, the body responsible for the survey has said.

A report from the National Records of Scotland (NRS), which conducts the census, proposes that individuals should be advised to answer according to how they self-identify, regardless of the details on their birth certificate or whether they have a gender recognition certificate.

The report refers to research that suggests three times as many trans and non-binary people would be willing to answer the sex question with self-identification guidance than with legal sex guidance. It concludes: “A binary sex question with self-identification guidance therefore supports participation for all people with the census and clarifies to data providers and data users the basis of the question.”

Before the NRS published its draft guidance, equalities groups argued that trans men and women should continue to be allowed to answer the compulsory sex question with the sex in which they live and identify, as they were in the 2011 census under guidelines that were less widely consulted on.

James Morton, the manager of the Scottish Trans Alliance, noted that trans men, trans women and non-binary trans people living in Scotland made up fewer than 0.6% of the population and their numbers would not affect the quality of census data analysis.

Critics say the move will put the accuracy of the data collected at risk by conflating sex and gender.

Eighty senior academics signed a letter sent to census authorities, the prime minister and Scotland’s first minister this month arguing that the draft guidance – similar versions of which are being considered for England and Northern Ireland – would effectively transform the longstanding sex question into a question about gender identity.

Dr Kath Murray, of the policy analyst collective Murray Blackburn Mackenzie, said the guidance presented “risks in terms of data reliability and consistency over time, as well as equalities monitoring”.

Murray said: “We are yet to see evidence of user demand for guidance which directs respondents to answer the sex question based on their self-declared gender identity, or that data users were meaningfully engaged in the question development process.”

She said similar guidance introduced in 2011 was not widely consulted on, and it was not clear how the quality of the resulting data was affected.

This month the Scottish government offered reassurance that changes intended to simplify how transgender people change the sex on their birth certificates would not diminish the rights of other women.

The issues of transgender rights reform continues to polarise opinion and has caused a significant rift within the Scottish National party.

The Scottish parliament voted in June to ask new voluntary questions about transgender identity and sexual orientation in the 2021 census, allowing national demographics to chart Scotland’s trans community for the first time. Two months later the NRS decided to retain a binary male/female sex question, after dropping a proposal to include a third option.

An NRS spokesperson said: “Following careful consideration of all of the evidence, NRS continue to recommend a binary sex question with self-identification guidance for the 2021 census. The final decision on the questions to be asked in Scotland’s census 2021 will be made by the Scottish parliament, as part of their consideration of the subordinate legislation, in 2020.”