The bomb exploded just before midnight and damaged the main entrance and front of the building. Such was the force of the blast that several nearby properties had its windows blown apart.
No one was seriously hurt but there was one person who had some minor injuries after being cut by shards of glass.
Police have been speaking to people in the area in the wake of the incident to try and determine what happened.
"There are some witnesses who said that someone was at the building and then ran away shortly before the detonation," said Stephan Söderholm, information officer with the Skåne police.
The justice centre has multiple departments including a courthouse, police offices, the region's prosecution authority and the economic crime authority for the area.
It also has secure hearing rooms and a remand centre.
In February the building was also attacked causing a similar amount of damage. On both occasions no known threats had been made in against the justice centre before the bombs went off.
Police have yet to confirm whether the two events are linked.
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"It is too early to make any connections. As far as I know there is no extra threats against the building right now," said Fredrik Svensson of the local police to Sydsvenskan.
Malmö has been hit by a string of bombings this year including several car bomb attacks.