In a mock exercise, the fake bomb was placed few metres away from the state Legislative Assembly complex, where the budget session is going on.
Goa Police, Indian Coast Guard, Navy and other security agencies have been executing Sagar Kawach exercise throughout the state to plug the security loopholes.
The exercise is in routine after Mumbai 26/11 attack.
Deputy Superintendent of Police N C Raikar told PTI that the decoy-terrorist entered the complex from behind by jumping the compound wall.
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The agencies will certainly look into the loophole and plug it, he said.
Eye witnesses revealed that the decoy terrorist managed to plant a fake bomb under the minister's car, which was parked in the basement of ministerial complex.
The decoy was reportedly stopped by security when he tried to enter into the ministerial block with the second fake bomb in his hand.
After failing to nab the decoy, police later continued their exercise by getting the bomb squad and sniffer dogs to diffuse the fake bomb.