A fundamental question about sefirat ha-omer is whether the mitzva is mandated by Torah law or rabbinical enactment while the Temple no longer stands. The Torah says, "And from the day on which you bring the omer of elevation offering – the day after the "Shabbat" – you shall count off seven weeks. They must be complete" (Vayikra 23:15).

According to Rosh, Ran, and many other Rishonim, the Torah commandment to count the omer applies only when the omer offering is brought on the sixteenth of Nisan in the Temple. Today, however, when we do not bring this offering, the mitzva is only mandated rabbinically. The Sages enacted that we continue performing this mitzva in commemoration of the sefirat ha-omer that was practiced in the time of the Temple. For this reason, right after counting, we customarily recite a short prayer for the rebuilding of the Temple. After all, when the Temple is rebuilt, we will once again be fulfilling a Torah commandment by performing this mitzva, not merely a rabbinic decree.

However, Rambam and Raavya maintain that the omer offering is mentioned in the verse only to teach us the date on which we begin to count the omer. It is not a necessary condition for the fulfillment of the mitzva. Therefore, the Torah commandment of sefirat ha-omer applies even today, when the Temple is in ruins and we are unable to bring the omer offering.

The practical ramifications of this dispute concerns situations of uncertainty. For example, if one counts during bein ha-shmashot (twilight, between shki’a and tzeit) it is questionable whether he fulfills the mitzva of sefirat ha-omer. If we consider bein ha-shmashot day, he does not fulfill his obligation, because the time for the next day’s count did not yet arrive. If we consider it night, however, he fulfills his obligation. Shulĥan Arukh (489:2) and the majority of poskim maintain that one who counts during bein ha-shmashot fulfills his obligation, because, in their opinion, sefirat ha-omer is a rabbinic mitzva nowadays, and we rule leniently in cases of uncertainty about a rabbinic law. However, many Aĥaronim write that it is proper to act strictly and count again, without a berakha, after tzeit, in order to fulfill the mitzva even according to those who maintain that sefirat ha-omer is a Torah commandment nowadays, and thus one must act strictly in cases of uncertainty (Eliya Rabba; mb 489:15; bhl 489:1, s.v. "lispor ha-omer").