Unfortunately the way that IEC 60601-1 is written is to consider voltages above 0.1V as unsafe, and then provide exceptions for voltages <60Vdc.
(I would prefer the other way around: consider up to 60Vdc safe in general, with special requirements when appropriate.)
Anyway, the main exclusion in IEC 60601-1:2005 is in Clause 8.4.2 c), which allows up to 60Vdc to be contacted without a tool. You will need prepare the RM document and instructions for use to meet the requirements detailed in the standard. There is a similar requirement in IEC 60601-1/A2:1995 under Clause 16 e), without the risk management.
If your device is used around fluids take care with the risk assessment, as this may be a case where some isolation is reasonable even for 3V (e.g. for a dental drill).
Once the exclusion in 8.4.2 is established, then there is no need for a means of protection to be evaluated for requirements such as earthing, leakage, dielectric strength, creepage and clearance (i.e. 8.6, 8.7, 8.8 and 8.9 are not applicable). This conclusion can be arrived at by the first sentence in Clause 8.5.1.1 (the exclusion for 8.7 can be found in Clause 8.4.2).
Test labs apply these exclusions all the time (both 2nd and 3rd editions), although possibly unknowingly. When a device has mains voltages (100-240V), these get all the focus and the secondary voltages (+5V, +/-15V, +24V etc) get largely ignored.
However, it seems that when there is no mains voltage around (i.e. battery operation only), some test labs feel uncomfortable having no tests for isolation, so suddenly 3V becomes dangerous and full isolation requirements get thrown at it. But this ignores the exclusions provided in the standard, is not reasonable nor consistent with testing of mains powered devices.
If your test lab is requiring 500V or 1000V isolation, gently discuss the above with them first (we all make mistakes), and if they don't agree look for another test lab.