REUTERS/Tobias Schwarz
Merkel also announced in her speech that her government would aim to replace the current law, which criminalises insulting foreign leaders.
Böhmermann, read out his offensive poem about Erdogan two weeks ago on German TV and made fun of an earlier German song that ridiculed Erdogan.
What Böhmermann did is illegal under German law - Erdogan pressed charges for insulting him personally- but the inquiry needed the approval of the German government to begin.
"There were different opinions between the coalition partners - the conservatives and the SPD (Social Democrats)," Merkel said, according to Reuters. "The outcome is that the German government will give the authorization in the current case."
Merkel insisted that the decision did not amount to a verdict on whether the comedian was guilty or not.
If found guilty, the comedian could face up to five years in jail for insulting a foreign head of state, and one year for defamation, according to Deutsche Welle.
The decision which was widely awaited has shocked people everywhere and the reactions started flooding social media straight away.
This can't be for real? "Angela Merkel agrees to prosecution of comedian over Erdogan poem" https://t.co/ZuhqNM5ThV
- Bente Kalsnes (@benteka) April 15, 2016
????? Chancellor Angela #Merkel approves indictment of TV satirist #Boehmermann. pic.twitter.com/zBMc2lCeX5
- Onlinemagazin (@OnlineMagazin) April 15, 2016
Hey @ #Merkel do you remember that we have freedom of speech??? https://t.co/7HZzi2jq1k
- lisa (@_cherrybombx_) April 15, 2016
This story gets worse and worse: "Angela Merkel agrees to prosecution of comedian over Erdogan poem" https://t.co/Z6Pp5AkDdw
- Jodie Ginsberg (@jodieginsberg) April 15, 2016
Merkel had initially defended the poem and has on multiple occasions during negotiation with Turkey insisted on the value of free speech. She later called the poem "deliberately offensive."