Start at the beginning
In most dojo's today, despite the various local languages that may be spoken in the surrounding area, the language of the dojo will often include some Japanese. One of the most frequent times that Japanese will likely be spoken is when the Sensei or one of the senior students is counting out loud. In fact learning to count in Japanese is really quite simple, and since these commands are used often, and repeated over and over again, at least up to the number ten, you are bound to catch on quickly.
Now if you are ever asked to count during the course of a class try to do so in Japanese, and always be sure and do so in a loud firm voice so that all those present in the dojo can clearly hear you, but be sure not to shout in an unseemly, or disrespectful manner. If you are counting to keep the rhythm to warmups for example, always remember to count during each excercise, this will help to keep both you and the class at a synchronized pace.
In order to learn count up to ninety-nine all you really need to know are the Japanese terms for the numbers 1 through 10 - after that it is just a matter of remembering to combine these numbers in a specific sequence to get the desired result.
The numbers from one to ten are pronounced as follows:


two ni
three san
four shi
five go
six roku
seven shichi
eight hachi
nine kyu
ten ju
Above ten the numbers are pronounced differently: for example the number 11 in Japanese is translated as "10 plus 1"
eleven ju ichi
twelve ju ni
thirteen ju san
fourteen ju shi
fifteen ju go
sixteen ju roku
seventeen ju shichi
eighteen ju hachi
nineteen ju kyu
Above the number twenty the numbers are again pronounced in a slightly different manner. For example the number 20 in Japanese translates as "2 - 10's" and continuing on therefore, the number 21 would be considered as "2 - 10's plus 1"
twenty ni ju
twenty-one ni juichi
twenty-two ni juni
and so on - all the way up to the number 99.
For example the number 56 would be "5 - 10's plus 6" - or - "gojuroku" - the number 61 would then be "6 - 10's plus 1" - or - "rokujuichi" and so on and so on.
The number 100 is pronounced as "hyaku" so counting above 100 is basically just a matter of adding the word "hyaku" in the appropriate place and then following the same general principle for example the number 150 is pronounced as "hyakugoju".
So give it a try, and learn to count with confidence, at least up to the number ten, since you will find that in most dojos the "count" during class will normally only go up to ten, at which point the count usually starts over again at the number one, with this pattern repeating it's self as often as maybe required by the sensei.
You just never know, one day you may find that you too are asked to count out loud for the benefit of the rest of the class, at which point being able to do so in Japanese just may make your task that much more interesting, and enjoyable.