The ward West Lothian, will continue to assess patients on weekdays but will have to transfer children to Edinburgh if they need to be admitted.
The decision, which was announced last month, was “not taken lightly” NHS Lothian said.
Trainee paediatric doctors were removed from the hospital in April, reducing the number of doctors available to provide out-of-hours cover. Shifts have been covered since then using the existing team and locum doctors.
The ward will return to a 24-hour, seven-day-a-week service on July 30.
The health board said it was not possible to secure enough staff for the three-week period.
From today, the ward will open Monday to Friday from 8am to 8pm as an assessment and programmed investigation unit but will close at weekends.
Arrangements have been made for transferring children to the Royal Hospital for Sick Children in Edinburgh if they need to be admitted following assessment or if they become ill during opening hours.
There will be no change to outpatient appointments and maternity and neonatal services at the hospital, the health board said.
Dr David Farquharson, medical director of NHS Lothian, said: “Reducing the service provided by the children’s ward on a temporary basis has been a very difficult decision to make, but the risks of not taking this action are too great.
“While staffing is in place to cover the shifts over the next three weeks, we have been unable to ensure that adequate back-up is in place should there be an unplanned absence.
“These temporary changes are to ensure we can maintain a safe and robust service for the children of West Lothian.
“The alternative, of crossing fingers and hoping for the best, is not good enough.
“It would risk a closure of the ward at the last minute, causing confusion for parents and staff and possible delays to emergency care - a risk we are not willing to take.
“I am confident that arrangements are in place to manage this temporary change to the service and that this is the safest option for patients.
“I would like to stress that full service will return on Monday July 30.
“We have reinforced our commitment to the children’s ward at St John’s hospital time and time again.”