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We recently had a repair done. the car was in the shop on two separate days. Although we did not ask, no estimate was offerred and the repair was over $600. Overall we were billed for 6.25 hours including smoko and coffee breaks. There was one period of time in which we were present that the car was unattended for at least 30 minutes. Yet we were billed for all that time. Is it legal to bill for downtime? The only time during the 2 day period that was deducted was 1/2 hour for lunch on one of the days.

It would not be usual to charge you for downtime. However, many franchise dealers work on Flat Rate Charging, which means if a job should take say 2 hours according to the manufacturer's Flat Rate manual, you will be charged 2 hours regardless of whether the technician takes 4 hours or 1 hour. In other words, you will not be penalised for an inefficient technician, but the repairer may gain from a particularly efficient technician.
In a situation such as yours, if you believe you have been overcharged, you should take this up with the workshop manager and ask for an explanation.

This was not flat rate, but based on the mechanic's personal time sheet showing he worked on the car from 9am - 2 pm. I/2 hour was deducted for lunch. I asked the workshop owner about charging for breaks and he told me that was their standard procedure.

The law requires a worker to be paid for tea breaks but the Consumer Guarantees Act requires that any charge made to a consumer for labour be "reasonable".
So there is no legal requirement for a repairer to charge you the actual time taken, but they must only charge a reasonable charge for the work carried out.
Given that this job took a few hours, as long as the charge made to you is reasonable for the work done, there is nothing preventing the repairer from charging you for the 10 minute tea break.
If you believe the charge made to you is not reasonable, you can have the matter heard at the Disputes Tribunal.

How would I know if it was "reasonable?" And their "tea breaks" seem to exceed 10 minutes. At one time my partner observed the car without attention (no mechanic present) for around half an hour.

Based on your questions, I'm assuming you think the amount charged to you is not reasonable.
An arbitrator at the Disputes Tribunal would mediate and on balance, if they agree with you (that the charge is not reasonable) they will find in your favour and the repairer will be ordered to make a partial refund payment to you.
However, don't base your argument on the fact that you (or your partner) observed the vehicle unattended for a period, as it has no bearing on the reasonable charge.

"However, don't base your argument on the fact that you (or your partner) observed the vehicle unattended for a period, as it has no bearing on the reasonable charge".

Agree, the garage could legitimately claim the mechanic servicing the vehicle had to obtain spare parts from a local supplier,