Human Rights Watch's director in Central Africa, Lewis Mudge, said the three girls were released from the Ngozi Central Prison two days after the release of Attorney General Aimée Laurentine Kanyana, told RTNB that their provisional release had been approved ,
The students were charged on 18 March for "insulting the head of state" and sentenced to five years in prison if convicted.
CNN could not immediately reach the Burundian government for comment on the case.
The arrest of the students led to an international condemnation of the Burundian government, with critics showing their support for the girls in social media with roughly drawn pictures of Nkurunziza and the hashtag #FreeOurGirls.
The girls, who are all minors, are part of a first group of seven people arrested earlier this month in Kirundo province in the northeastern African nation.
3-year-old girl was released because she was under the age of criminal detention, while three others were also letting go.
School children in Burundi were previously detained for similar crimes.
Burundi arrested eight secondary school students who allegedly offended Nkurunziza by using phrases like "Get out" or "No to 3. Semester "on a picture of him in a textbook wrote o Human Rights Watch.
In the same year, hundreds of children were banned from the schools because they scribbled the President's face in their books.
Nkurunziza, who has been in office since 2005, was re-elected to a third term in 2015 despite massive protests and concerns over the legality of his second term being exceeded.
But Burundi's Constitutional Court ruled that he was eligible because, in his first term, he was elected by Parliament, which was not elected by the people.
Results died in the violence that worsened the 2015 vote.
"Authorities should focus on bringing perpetrators of serious violations to justice instead of imprisoning students for scribbles."
In early March, UN High Commissioner for Human Rights Michelle Bachelet said that the agency was forced to close its office 23 years under pressure from the Burundian government.