"In a country under the rule of law, it is not up to the government to decide," Merkel said. "Prosecutors and courts should weight personal rights against the freedom of press and art."
Although Böhmermann could face several years in jail if convicted, lawyers familiar with similar cases expect that the comedian would have to pay a fine, if at all.
The stakes are potentially higher for Merkel.
Criticism of her reaction to the incident had mounted ahead of the announcement. Opponents have said the chancellor made a glaring misstep earlier by calling the poem "deliberately offending" — a comment interpreted by some as support for Erdogan, who has been accused of cracking down on press freedom in Turkey.
Not allowing the charges to proceed could have jeopardized a refugee deal with Turkey, which was recently negotiated. Turkish officials had publicly pressured Merkel to allow the charges. Earlier this week, Turkey's deputy prime minister, Numan Kurtulmus, said that the poem was a slap against all Turks.
"That is why the Republic of Turkey demands that this impertinent man is immediately punished for insulting a president, within the scope of German law," Kurtulmus said. He went on to call the poem a "serious crime against humanity" that had "crossed all lines of indecency."
In her statement Friday, Merkel tried to appease critics by announcing that she would seek to repeal the controversial German law against insulting heads of state.
Merkel was forced to decide on the matter after the Turkish president had officially filed charges against Böhmermann earlier this week. The mock poem in question aired during a segment of ZDF Television's Neo Magazin Royale show last week. Some of the lines included accusations of bestiality and other unsavory things.
Merkel's decision followed clashes within her own government.
Germany's Social Democrats, the chancellor's coalition partners, wanted to prevent a court trial. One of the party's leading politicians, Thomas Oppermann, said prosecution for satire "does not fit into a modern democracy."
Another dissenter, Foreign Minister Frank-Walter Steinmeier, called free expression "among the most important values protected by our constitution.”
Udo Vetter, a defense lawyer and blogger, commented that Merkel's decision sends the wrong message. “It forces Germany's legal authorities to act on behalf of Mr. Erdogan,” Vetter argued. But an internal report commissioned by the foreign ministry concluded that Böhmermann was most likely guilty of a criminal offense, according to Berlin's Tagesspiegel newspaper.