More than 1,500 companies have failed to report their gender pay gap figures before Wednesday night's deadline.
The Equalities and Human Rights Commission said 1,557 firms had missed the deadline.
It will now contact these companies to remind them of their legal obligations.
The equalities watchdog will investigate those firms that fail to comply and could take legal action against them, with penalties including an unlimited fine.
All companies, charities and public sector bodies with more than 250 employees were required to submit their gender pay figures before Wednesday's deadline.
The EHRC will check whether those firms that failed to report fall into this category.
One organisation that missed the deadline was the Unite union, which belatedly published its figures on Thursday.
The union, which describes itself as being "at the forefront of the trade union campaign to achieve equal pay", revealed that its female employees' median hourly pay was 29.6% lower than what male workers are paid.
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More than 10,000 firms have published data, with in excess of 1,000 firms reporting on the last day.
More than three-quarters of UK companies pay men more on average than women, BBC analysis of government figures suggests.
The median pay gap among those companies was 9.7%.
The figures indicate 78% of firms pay men more than women on average, while 14% pay women more.
This is based on the median measure, which is the level of pay that separates the top half of earners from the lower half.
In total, 8% said they had no pay gap between men and women.
The gender pay gap is not the same as having unequal pay, which would be against the law. By law, men and women with the same jobs have to be paid the same wages.
A gender pay gap can arise if there are more highly paid men than women in a company, or if women are deemed to be less experienced than their male counterparts, or if women take a hit to their salary after taking maternity leave.
In reporting gender pay, firms with more than 250 staff have to publish data on the average difference between male and female employees.