Pro-Palestinian protesters started shouting as foreign minister Maria Malmer Stenergard returned to her seat after addressing parliament, lawmaker Ann-Sofie Alm told AFP.
"They started screaming and making a ruckus in the gallery... then someone throws an object over us parliament members," Alm said, adding that the object was thrown "at the foreign minister".
According to Swedish media, the object landed two rows behind the Stenergard, who left her seat and quickly left the room.
"I see how Maria is reacting to the thud and runs out of the room," Alm said.
Several media said the bag contained tomatoes. Alm told AFP she had not seen the contents but described it as a "bag with a red squishy substance inside".
The parliament speaker called on security to remove the protesters and temporarily halted the debate.
News agency TT reported that three people were detained by parliament security and handed over to police.
Prime Minister Ulf Kristersson condemned the actions of the protesters.
"I now expect a thorough analysis of how this could happen and strong measures to maintain the security of MPs and ministers in the chamber," Kristersson told TT.

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