Emirati medical interns in Ministry of Health hospitals will receive a monthly stipend that is half the amount a starting doctor would make.
Seven months ago, the ministry decided to stop paying dozens of Emirati interns in hospitals and clinics in the Northern Emirates.
The interns appealed directly to the minister, Abdul Rahman Al Owais, for help.
Mr Al Owais had said there was no budget for salaries, but they could receive financial rewards or "bonuses" by the end of the year. He also said the interns were trainees and so should not be paid.
The National reported recently that junior doctors and members of the FNC were pushing the ministry to resume pay for interns.
Yesterday, the ministry decided interns will be paid retrospectively to the start of the year.
According to a statement, Mr Al Owais said the decision was made to coincide with regulations in Abu Dhabi and Dubai, and to provide interns with "an appropriate and convenient working environment during their internship year".
Yesterday's edition of Al Ittihad quoted Anood Sulaiman, the director of human resources at the ministry, as saying interns will be paid about Dh11,000. Starting salaries for doctors is Dh22,000.
Interns in hospitals under the Health Authority - Abu Dhabi are paid Dh30,000 a month. The Dubai Health Authority also pays its interns.
All hospitals in the Northern Emirates are managed by the ministry.
While interns said they were grateful to be paid, they were disappointed by the amount.
"Happy about this decision? We are actually shocked," said Dr Salma, a graduate of Sharjah University who commutes daily from Dubai to Fujairah for her internship.
"We take on all the responsibilities of a regular doctor, from consultations to prescribing medications and even working in the emergency department.
"We work daily and every few days we're required to work a 24-hour shift. We also have to work two full weekends every month.
"And at the end of all this we're only paid half a doctor's salary. My question to the ministry is why?"
Dr Faisal, from Sharjah, said many questions remained unanswered.
"This is a wonderful effort by the ministry and I'm thankful, but it's only the first step," Dr Faisal said. "We work full time yet we are only paid half.
"And after this year is over, what's next? There is no guarantee that we'll be hired when we're done. We need more clarity on what comes next."
Emirati doctors said further action was needed to motivate UAE nationals to work in the healthcare industry.
Dr Asma Al Nuaimi, a paediatric pulmonologist at Zayed Military Hospital, said the stipend was a good start.
"Interns are required to work full time, so it is natural that this is a paid job," said Dr Al Nuaimi said. "It will definitely encourage more Emiratis into the field."
But she said many nationals perceived medicine as a field that required high investment but offered little return, she said.
"The number of Emirati doctors now is very low," Dr Al Nuaimi said. "Many feel that the amount of energy they're putting in is not that same as what they're getting out of it.
"Of course, there is always the moral aspect and a sense of helping the community, but the salaries need to be reasonable as well.
"Elsewhere, a doctor is considered a prestigious individual, someone who stands apart from other members of the community. The same amount of respect needs to be given to doctors here.
"Of course this cannot be done in a day. It is something that will take time and is always evolving."
The ministry was not available for comment.
(Interns' names have been changed at their request).