The court also awarded Giržadas a compensation of LTL 20,000 (over EUR 15,000).
The court also canceled two orders by former Minister of the Interior Raimundas Palaitis on candidate verification and dismissal as running counter to existing legal acts.
The court ruling is not final and can be appealed to the Lithuanian Supreme Administrative Court within 14 days.
The court did not say that Giržadas must be reinstated promptly or immediately, and Giržadas noted the fact. He plans to consult his lawyer on the execution of the court ruling.
Former FCIS Director Vitalijus Gailius has also turned to court over his dismissal.
They were both sacked by the then Minister Palaitis on 15 February based on information received from the State Security Department.
Palaitis later resigned after coming under criticism of the ruling conservatives.
Kęstutis Jucevičius currently heads the FCIS. The Chief Official Ethics Commission has ruled that he has confused public and private interests.
Commenting on the court ruling, Lithuanian Prime Minister Andrius Kubilius said the court at least partly corrected the mistake of ex-Minister of the Interior Raimundas Palaitis.
„I have always considered that the hasty and unjustified dismissal of the FCIS heads was Minister Palaitis' mistake," Kubilius told BNS on Tuesday.
President Dalia Grybauskaitė has said Palaitis sacked the FCIS heads pursuant to procedures stipulated by the law.
"The examination cast a shadow of suspicions upon both FCIS leaders. Reputation of top officials of law-enforcement institutions should raise no doubts. The minister followed the law," the president has said.