Consolidated analysis of responses to a similar question on
Tortoise Forum and Hermann Tortoise:
Environment
For a question such as this, you should supply your habitat.
- diet
- substrate
- measured temperature
- measured humidity
Substrate Issues
- The tortoise could be allergic to your substrate
- changing to kitchen towels or newspapers can single out this issue.
- The substrate could be too dry and might require additional humidity.
- loose substrate could have become lodged in the tortoise's nasal cavity
Poor Humidity
Wheezing and clicking can occur with Redfoot tortoises when they lack proper humidity or are kept too dry.
- ensure he doesn't feel light or have dry, flaky skin; this can indicate dryness.
- if the eyes of the tortoise are slightly watery; this can indicate dryness.
- increase the humidity; try for 80%. You can use a digital hygrometer.
- provide access to a warm, fresh, water bath at least once daily
If you are concerned about shell rot due to increasing humidity, ensure the enclosure is kept clean and periodically clean your tortoise lightly with a soft toothbrush.
General Dehydration
- ensure the water content of foods is sufficient
- ensure water is available
Illness / Disease
- whistling when breathing may indicate a respiratory infection or pneumonia.
- Metabolic Bone Disease (MBD) causes shell deformity, which could create breathing irregularities.
- if you suspect either of these, consult a professional veterinarian, as medications may be needed
Normal Whistling
Some red-footed tortoises just whistle regardless of humidity and health.
Conclusion
In your particular case, I suspect this is due to humidity, but we would need more data and an implementation of a humidity plan to conclude this.