Flag qubits have recently been proposed in syndrome extraction circuits to detect high-weight errors arising from fewer faults. The use of flag qubits allows the construction of fault-tolerant protocols with the fewest number of ancillas known to-date. In this work, we prove some critical properties of CSS codes constructed from classical cyclic codes that enable the construction of a flag fault-tolerant error correction scheme. We then develop fault-tolerant protocols as well as a family of circuits for flag fault-tolerant error correction and operator measurement, requiring only four ancilla qubits and applicable to cyclic CSS codes of distance 3. The measurement protocol can be further used for logical Clifford gate implementation via quantum gate teleportation. We also provide examples of cyclic CSS codes with large encoding rates.