The strike is over a 1% pay rise that was awarded last year to all midwives in England, Scotland and Wales.
The Department of Health said officials worked to ensure a safe service was provided during the stoppage.
It said midwives in Northern Ireland had the same settlement as colleagues in England.
"While we would like to be in a position to have done more in 2014/15, it is important to recognise midwives and other non-medical staff received a minimum of 1% extra with the average rise through incremental progression being 3.7% and some staff receiving 6.7% more," a spokesperson said.
While the most senior midwives in Northern Ireland got the rise in a one-off payment last March, those on lower pay bands did not.
Instead, most received the annual uplift of around Â£1,500.
According to the Royal College of Midwives (RCM), all midwives should receive the 1% increase like elsewhere in the UK, regardless of their band, as well as the uplift in salary that is built in to the pay system.
It has emerged that talks resumed on Tuesday between the Department of Health and some of the health unions.
While those negotiations have been described as positive, further industrial action is planned, including claiming for all overtime.
Amy Leversidge of the RCM said the department was "being cheeky" to suggest that midwives in Northern Ireland had received the same pay rise as their English colleagues.
She said staff on higher pay bands had received a 1% "temporary uplift" to their basic pay in February, but at the start of the financial year in April, their pay went back to 2013 levels.
Incremental progression based on experience and performance was a part of the NHS pay structure rather than a pay rise, the union's employment relations adviser said.
"We don't want to wait until February 2016 to find out what's happening - we want to negotiate a solution now," she said.
Midwife Hazel McAllister told the BBC: "We are not any less passionate, caring or hard-working than colleagues in other parts of the UK who have gained this 1% pay rise.
"We feel very undervalued by the powers-that-be who have refused to pay this.
"I have been a midwife for 37 years - it's a fantastic profession but I would worry about its future."
Midwives in Northern Ireland staged a four-hour strike from 08:00 BST and 12:00 BST on Thursday in a pay dispute.