Do it by checking the remainder of dividing by 3:
$minute = date('i');
if($minute%3==0){
//if minute is 0,3,9,12,15...do something
}else if($minute%3==1){
//if minute is 1,4,10,13,16...do something
}else if($minute%3==2){
//if minute is 2,5,11,14,17...do something
}