Stanisław Wziątek made the statement in an interview with public broadcaster Polish Radio on Thursday.
The suspect was arrested at the defence ministry on Tuesday. On Wednesday, he was charged with spying for a foreign intelligence service.
The man was then detained for three months, at the request of prosecutors.
Asked about the case, Wziątek told Polish Radio the suspect had been working for a strategic department at the ministry, where he was responsible for "simple administrative tasks."
He added the man "seemingly didn't have access to top secret information," such as military plans, but could have come into contact with them in one way or another.
Wziątek said the suspect "wouldn't have been arrested without a good reason."
He added that prior to the arrest, the suspect was subject to comprehensive surveillance.
Asked if three months would be enough to finish the investigation, Wziątek said the period may turn out to be too brief.
He added much would depend on whether the suspect would be "willing to cooperate" with investigators, providing information about contacts with individuals and groups with whom he had been talking.
Wziątek said the probe should explain the circumstances in which the suspect started to spy for a foreign intelligence service.
Uncovering the motivation behind his actions will allow investigators to take the next steps in the probe, which may lead to "a whole group of spies" being caught, Wziątek said.
"If he indeed is a spy, he couldn't have been acting alone," he added.
The suspect had been working for the Ministry of Defence's Department of Strategy and Defence Planning, Polish state news agency PAP reported.
He was charged with acting on behalf of a foreign intelligence service.
On Tuesday, Jacek Dobrzyński, the spokesman for Poland's minister for security services, said the Military Counterintelligence Service (SKW) had gathered "powerful, damaging information" confirming the man had been spying for a foreign intelligence service.
The suspect faces a prison sentence of between eight years and life's imprisonment.
(pm)
Source: PAP