A kohen often comes to my minyan and even if he is early, he says Shemoneh Esrei together with the chazan and does not perform the mitzva of Birkat Kohanim (=BK). I understand that he is allowed to break his prayers to do BK and then to return to his place. He claims that what he does is fine according to a different opinion. Who is correct? Answer:
The question of BK during Shemoneh Esrei is a complex one that can depend on several factors. The mishna (Berachot 34a) states that a chazan should do BK if he is the only kohen there and he is confident that he can return to complete chazarat hashatz without confusion. The implication, as the Shulchan Aruch (Orach Chayim 128:20) rules, is that if there were another kohen available, the chazan would not recite BK. The Radbaz (IV:293) reasons that the same thing should be so for one in the middle of his personal Shemoneh Esrei – if and only if he is the only kohen should he go up. The Magen Avraham (128:40) accepts the Radbaz, and this is the first opinion cited in the Mishna Berura 128:106).
291 - Receiving Video of Personal Event on Shabbat
292 - Birkat Kohanim for a Kohen who is in Shemoneh Esrei
293 - Dancing at a Wedding during your Sefira Period
However, many disagree with this Radbaz and Magen Avraham. The Rav Pealim (III, OC 4) points out that in the mishna’s case, the chazan is up to the point of Shemoneh Esrei in which BK is recited. If he is anywhere else in Shemoneh Esrei, we can say that BK is a hefsek (improper break). Indeed, a second opinion in the Mishna Berura makes this distinction, ruling that only if the kohen is up to the correct place for BK does he recite it, and this is the opinion that seems prevalent today (see Tefilla K’hilchata 14:35; Yalkut Yosef, Birkat Kohanim 21).
Your question implies that since the kohen says Shemoneh Esrei "along with the chazan" (a system that has certain advantages for some somewhat slow daveners – beyond our scope) he would be up to the right place. Then, almost all agree that he should do BK when he is the only kohen. If so, we do not know why he is reluctant to do this. However, there are two factors that impact whether he is required to do so.
First, one whose tefilla will be confused by doing BK (see aforementioned mishna, Berachot 34a), does not recite BK (Sha’ar Hatziyun 128:83). (Admittedly, it is hard to know what qualifies as being confused). Yalkut Yosef (ibid.) does cite an opinion that confusion applies only to a chazan, as everyone will be waiting for him to resume tefilla, and not to an individual. However, the Pri Megadim (Eshel Avraham 128:40) is among the more accepted opinions that confusion plays a role here as well.
Another factor is that the obligation to do BK has to be activated in a timely fashion. One violates his obligation for BK only if he has been called to do so, based on the pasuk in this context "amor lahem" – say to them (see Beit Yosef, OC 128). There is another halacha that a kohen can do BK only if he stepped toward the duchan during the beracha of R’tzei (Sota 38b). So if this kohen failed to move forward at least a little bit at that time (he may do so during Shemoneh Esrei, but the kohen in question presumably does not), he is disqualified. Realize that usually a kohen is not called until right before BK (if he is the only kohen, he will not be called at all – Shulchan Aruch ibid. 10.). So for those who did not step forward, it will be too late to obligate them. It is strange, then, that some poskim, including the Radbaz (ibid.) discuss a Torah obligation of BK superseding the Rabbinic mitzva of Shemoneh Esrei even before he is called (Halachot Ketanot I:64 points out this difficulty). It is difficult to say that the kohen violates his obligation if he does not prepare himself for BK on time. In theory, someone could force the issue by telling your kohen earlier in chazarat hashatz to prepare himself (based on Magen Avraham 128:40). However, we do not think that this is appropriate behavior.
So, one might encourage the kohen to find the best way to make BK possible (see Living the Halachic Process vol. IV, A-16). However, we do not think he should be shamed into doing so when he might have a reason not to.