There are two methods of calculating FBT on a company car that you can choose from:

1. Statutory Formula Method
2. Operating Cost Method

You can alternate between the two from year to year, so I recommend picking the method that provides you with the lowest taxable value.

Statutory Formula Method:

Vehicle Base Cost x Statutory Rate x Holding Period - Contribution Collected

In this formula: 

Vehicle Base Cost is the price to purchase the vehicle. 
The statutory rate is the rate provided by legislation. (All leases have a rate of 20%)
Holding Period is the amount of time the vehicle was available for use. 
Contribution Collected is any post-tax deductions you received during the year. 

Example: 

A leased vehicle with a Base Cost of $50,000 and packaged for the entire year would be calculated as so:

$50,000 x 20% = $10,000

If you received any deductions during the FBT, you would subtract that from the $10,000 taxable value. 

Operating Cost Method 

Total Operating Expenses of the Vehicle x (100% - Business Use Percentage) - Contribution Collected.

In this formula: 

Operating Expenses are the total costs of the vehicle for the year. (For example, a lease and all running costs.)
Business Use Percentage is calculated based on the number of km drove for business use as a percentage of overall driving during a 12 week period in which a logbook is kept. (To qualify, you must have held an ATO compliant logbook for at least 12 weeks. 

Example: 

A vehicle lease with $20,000 in total costs that has a registered business use of 90% would be calculated as so: 

$20,000 x (100% - 90%)
$20,000 x 10% = $2000

If you received any deductions during the FBT, subtract that from the $2000 taxable value. 

There's also a Fringe benefits tax calculator on the Australian Taxation Office website that's extremely useful. I hope that answered your question :)