"We cancel the appointment as we now know they are unwanted. We did it because we just think it's good for our ministry," Health MinisterThan Aung told 7 Days newspaper.
The ministry's appointment on Friday of three military officers to deputy director general positions sparked anger among tens of thousands of doctors and nurses in the country as well as abroad.
Starting Friday night, more than 33,000 petitioners participated in an online campaign against what they called the "militarisation" ofthe Health Ministry.
The government has been criticised for appointing former army officials to the posts of permanent secretary in almost all ministries. In these positions, they will serve as department heads in the transition period before the next government takes power after the November 8 general elections.
The government was also criticised for appointing military officers in organisations such as the Myanmar Red Cross Society and Fire Service Department.
A petition calling for reforms in the Union Election Commission (UEC) chaired by former army general Tin Aye was submitted to the government in February as it added an increasing number of former officers to the organisation.
In 2014, at least 100 army officers were appointed to UEC.
"It's too bad that president ignored our call for UEC reform," said Kyaw Myat from the Mass Movement Acceleration Network (MMAN).