Does state secrecy contradict the principle of government transparency?

In civics class, many students are taught that a classically liberal republic governs according to the principle of transparency. As every citizen has equal rights, every citizen has an equal right to know exactly what it is that the government is doing. According to this understanding, if only a tiny minority of citizens know what the government is doing, whereas the rest of the public is deliberately kept in the dark about such actions, then there is an imbalance of power, which is inconsistent with the principles of a liberal republic or liberal democracy. And yet every functioning republic, including the United States, has intelligence agencies that maintain classified information hidden to the public. Such information is hidden from the public on the grounds that such secrecy is necessary for defending the public from military threats. And yet such secrecy, it seems to me, contradicts the principle of transparency that is supposedly inherent to the idea of a liberal republic. Does any secrecy on the part of a government contradict the principles of classical-liberal republican transparency? Can state secrecy and classical-liberal republican transparency be reconciled?