Prueba así:
Código PHP:
<script type="text/javascript" language="javascript">
<?php $bidimensional_array = array(array(1,2,3),array(4,5,6),array(7,8,9)); ?>
function crear(){
var datos = new Array(<?=count($bidimensional_array)?>);
<?php
foreach($bidimensional_array as $key=>$sub_array){
echo "datos[$key] = new Array(".implode(',',$sub_array).");";
}
?>
//test del array en javascript
for(var i=0;i<datos.length;i++){
for(var j=0;j<datos[i].length;j++){
alert('datos['+i+'].array['+j+'] = '+datos[i][j]);
}
}
}
crear();
</script>
Saludos...