The IRASR has many projects associated with the operation of the new AUT radio telescope station. High precision atomic clocks, oscillators regulated by the atomic properties of matter play a vitally important role in the systems operation. Like any similar device, there are errors and a limit to the precision of the behaviour of these oscillators. The Allan variance is a well-known means to characterise frequency oscillators and clocks, especially for those measurement instruments of ultra-high precision. By taking advantage of the rapid application development approach, a system has been implemented within the Matlab® development environment for the measurement of Allan variance. Three major atomic frequency standards, a Rubidium atomic clock, GPS disciplined clock, and Hydrogen Maser, were utilised as the source of references in experiments that tested the developed system. Although the system developed finally meet all project requirements, the AVAR plotting results for different atomic frequency standards show that there is uncertainty on the level for specific tau. Thus, some limitations and recommendations have been identified to assist any future experimentation in this field.