Salwan Momika, a refugee from Iraq, has led several Quran-burning events in recent months, saying he wants to protest against the whole institution of Islam and ban its holy book.
“Yesterday, the Migration Agency decided to recall his status and residency permit and decided that he should be deported,” a spokesman for the Swedish office told Reuters.
He said the reason was that the man had given false information on his application for residency.
However, the spokesman said Sweden could not carry out the deportation order as the man would risk torture and inhumane treatment if he were to be sent back to Iraq. If the situation changes, the man will be deported, he added.
In July, the agency said it was re-examining Mr Momika's residency permit.
Protests in region against desecration of Quran in Sweden – in pictures
“I am not leaving Sweden. I will live and die in Sweden. The Swedish Migration Agency has made a serious mistake. I suspect there are hidden political motives behind this decision. I will appeal,” Mr Momika told Swedish public broadcaster SVT.
Anti-Islam activists have burnt several copies of the Quran in Sweden and Denmark, two of the most liberal countries in the world that allow criticism of religion in the name of free speech.
Many Muslims view desecrating the Quran as a grave offence.
Stockholm raised its terrorism alert to the second-highest level in August and warned of an increase in threats against Swedes at home and abroad following the Quran burnings.
Last week, a Tunisian gunman killed two Swedish football fans in Brussels in an attack which Sweden's Prime Minister said showed that Europe must bolster security to protect itself.
The gunman identified himself as a member of ISIS and claimed responsibility in a video posted online.