Yes you can be required to take a PT test while on profile. For it to be a valid test, you must perform one of the aerobic events: run, bike, swim, or walk. If you take an alternate aerobic event you must be given at least 90 days to practice that event. If you believe that this action is endangering your health I recommend you have a face to face meeting with your 1SG and CDR. You need to prepare for this meeting by putting together your facts and concerns. You must ensure that your discussion with the command team is professional and unemotional.
You should also provide a recommended solution such a time when you believe you will be fit enough to take a PT test. You can also discuss the issue with your medical provider and he may increase your profile in a manner that prohibits a PT Test. Keep in mind that the Commander can override the doctor’s profile but he will assume responsibility for your welfare by doing so.
I suggest you read: AR 350-1 and AR 40-501 Chapter 7
Personnel will be excused from physical fitness training only during periods of temporary or permanent medical limitations established in accordance with AR 40–501.
Personnel who cannot take part in physical fitness training because of a profile condition will be placed in rehabilitative programs and, within profile guidelines given by health care personnel, be supervised by the commander.
The APFT consists of pushups, situps, and a 2-mile run, done in that order on the same day. To be considered a record test, these events must be completed within two hours from the start of the pushup event until completion of the 2-mile run or alternate aerobic event. (See repetition and time guidelines in FM 21–20.) Record APFT scores will be annotated on a DA Form 705 (Army Physical Fitness Test Scorecard). For Soldiers on a permanent profile or an extended temporary profile (more than three months), a record test must include an aerobic event. The only approved aerobic events are the 2-mile run, 800-yard swim, 6.2-mile bike ride (stationary or track), or the 2.5-mile walk. Soldiers on permanent profile or a temporary profile of long duration (more than three months) will receive point scores for only those events taken. For example, if a Soldier has a permanent profile for the 2-mile run event and score 70 points in the pushup, 85 points in the situp and receives a “GO” for the 2.5 mile Walk, he will receive a score of 155 points in the total score column of the DA Form 705
Personnel with permanent medical profiles that preclude participation in the pushup or situp event will take the remaining events if a physician or physician’s assistant approves. The 2-mile run event, or an approved alternate test event as outlined in FM 21–20, must be taken if the test is for record. The alternate test is for Soldiers with permanent physical profiles that prevent them from running 2 miles. Soldiers with temporary profiles of long duration (more than 3 months) may also take an alternate test if approved by the commander and health care personnel. Soldiers must be given 3 months to prepare for the alternate test from either the date of the profile or the date recommended by health care personnel.
In closing please keep in mind most leaders want to do what is right for the Soldier and Unit. Therefore it is important to try to understand what your leadership is trying to achieve, why are they trying to achieve it, and what is the best way you can assist in resolving the issue at hand. I have never met a leader who would intentionally hurt one of their Soldiers. Sometimes it may feel like a leader is focusing on you but usually from the leader’s perspective they are just trying to make you a better Soldier.
The question is are their methods correct? This is where you need to be professional and discuss the issue with them from a knowledgeable position and present a reasonable solution. If you do not feel you are getting a fair shake after speaking to the CO Command Team then request to see the BNCSM/BNCDR on open door policy.