Turkey's foreign minister condemned the burning of several pages from the Koran in Sweden on Wednesday as "vile" and "despicable".
A man carried out the protest outside Stockholm's main mosque after Swedish police granted a permit for the protest, which coincided with the start of the Muslim holiday Eid al-Adha.
"I curse the despicable act committed against our Holy Book, the Holy Koran, on the first day of Eid al-Adha," Turkish Foreign Minister Hakan Fidan said on Twitter.
"It is unacceptable to allow these anti-Islamic actions under the pretext of freedom of expression.
"Turning a blind eye to such atrocious acts is to be complicit," he added.
Salwan Momika, 37, who fled from Iraq to Sweden several years ago, had asked police for permission to burn the Muslim holy book "to express my opinion about the Koran".
Ahead of the protest, Momika told news agency TT he also wanted to highlight the importance of freedom of speech.
Momika stomped on the Koran, put strips of bacon in it, and set pages on fire before slamming it shut, and kicked it while waving Swedish flags.
The police authorisation for the protest came two weeks after a Swedish appeals court rejected the police's decision to deny permits for two demonstrations in Stockholm that were to include Koran burnings.
Police had at the time cited security concerns.
A burning of the Muslim holy book outside Turkey's embassy in January led to weeks of protests, calls for a boycott of Swedish goods and further stalled Sweden's NATO membership bid.
Similar acts have in the past sparked violent protests and outrage across the Muslim world.
Ankara took particular offence that police had authorised the January demonstration.
Turkey has blocked Sweden's NATO bid due to what it perceives as Stockholm's failure to crack down on Kurdish groups it considers "terrorists".