Warsaw's district court argued that, since the cross had not been met with any objections in the past, it was accepted by most Poles and did not violate their rights.
It was placed in the chamber by two conservative politicians in 1997.
The court also chastised the Palikot's Movement party, led by former vodka tycoon Janusz Palikot, which brought the case, accusing it of calling for tolerance yet failing to show acceptance of religious symbols.
The party has tapped Poland's growing secularisation to become the country's third-largest political force. It said it would appeal the decision.
"The court failed to show objectivity," said Andrzej Rozenek, one of the party's parliamentary deputies."We are determined, so the path should take us all the way to Strasbourg," he said, referring to the European Court of Human Rights.
Rightist politicians said the decision reflected the feelings of most Poles. "This case was a grotesque joke," said Andrzej Jaworski, a deputy of the opposition Law and Justice Party and head of the party's committee to fight atheism.
Palikot's party includes Poland's first trans-sexual deputy and its only openly gay one and its agenda includes the legalisation of marijuana and same-sex partnerships. It claims the cross violates the Polish constitution and influences parliamentary decisions.