Ms Harman has launched a new Equalities Bill
Labour deputy leader Harriet Harman has been criticised by an official watchdog for exaggerating the pay gap between men and women.
UK Statistics Authority chief Sir Michael Scholar said Ms Harman's use of figures was potentially misleading.
She had said women were on average paid 23% less per hour than men but the Office for National Statistics (ONS) said the figure was actually 12.8%.
The government said Ms Harman's figures related to full and part-time workers.
The Government Equalities Office, which issued a press release in April with the 23% figure in it, said this provided the "fullest picture" of the gender pay gap.
'Impartial and objective'
But in a letter to Ms Harman, who is also the women's minister, Sir Michael said the use of different figures was "likely to confuse the general public".
He said: "The Statistics Authority is concerned that this may undermine public trust in official statistics."
"It is the Statistics Authority's view that the use of the 23% on its own, without qualification, risks giving a misleading quantification of the gender pay gap."
A source said Ms Harman's department was warned about using the figure beforehand but went ahead anyway.
Both figures were taken from the same annual survey of hours and pay, and are based on average hourly earnings excluding overtime.
The ONS measure is based on full-time earnings alone while the GEO figure includes full-time and part-time workers.
Both men and women who work part-time are paid less, but the vast majority of part-time workers are women. That means including all part-time workers in the figure could exaggerate the pay divide.
Sir Michael said neither measure was "entirely satisfactory" on its own and suggested different ways to discuss the gender pay gap that were "impartial and objective".
Knife crime row
But a spokesman for the Government Equalities Office rejected the criticism.
He said: "We understand the concerns raised about different measures of the gender pay gap - that's why we discussed this with the Office for National Statistics some time ago.
"The 23% gender pay gap figure used by the Government Equalities Office includes both full- and part-time employees.
"With women representing over three-quarters of the UK's part-time workforce, we believe this figure gives the fullest picture of the country's gender pay gap."
Last year the Home Office was rebuked by Sir Michael for a press release on knife crime statistics that he said was "premature, irregular and selective".
The row came as Ms Harman launched her Equalities Bill, which aims to establish an "equality duty" on public bodies.
Organisations such as schools and hospitals with more than 150 employees would have to report annually on their gender pay gap and they would have to promote equality in age, religion or belief, race, disability, pregnancy and sexuality under the proposed legislation.
Launching the Bill in the Commons on Thursday, Ms Harman said it would also outlaw the British National Party's "apartheid" membership rules, which dictates that members must be from the "indigenous British ethnic groups deriving from the class of 'Indigenous Caucasian"'.
Ms Harman said she was "shocked and horrified" by the election of BNP leader Nick Griffin and Andrew Brons to the European Parliament last week.
She said there was "no place" in Britain for having a political party that only accepted white people as members and the Equality Bill would prevent this.