The view of the vast majority of the Rishonim, and the generally accepted position, is that the Torah obligation of sefirat ha-omer applies only in the times of the Beit Ha-mikdash. Since the Torah requires counting “from the day you bring the omer of waving” (Vayikra 23:15) – referring to the special offering of the first portion of newly harvested grain, on the 16th of Nissan – this requirement is fundamentally linked with the omer offering. As such, the mitzva to count the omer does not, on the level of Torah obligation, apply after the Temple’s destruction, when we do not bring this sacrifice. We observe this mitzva only on the level of Rabbinic enactment, as opposed to Torah law. This is the view taken by Tosafot (Menachot 66a), the Ran (Pesachim 28a in the Rif), and many others. This is in contradistinction to the view of the Rambam, who famously writes in Hilkhot Temidin U-musafin (7:24) that the Torah obligation of sefirat ha-omer applies “in every place and in every time,” irrespective of the korban ha-omer. As mentioned, the commonly accepted view is that of the majority of Rishonim, who viewed sefirat ha-omer as a Rabbinic obligation in the absence of the Beit Ha-mikdash. (See Bei’ur Halakha, 489:1).
In light of the majority view among the Rishonim, some halakhic authorities have called into question the text of the “Hineni mukhan u-mezuman” prayer that many have the custom of reciting before counting the omer. In this prayer, we announce that we are prepared “to fulfill the affirmative command of counting the omer as it is written in the Torah, ‘You shall count for yourselves…’” We describe the mitzva as a “mitzvat asei” – a Biblical command – and proceed to cite the Scriptural source. Seemingly, this description of sefirat ha-omer reflects the Rambam’s position, that we observe the mitzva today on the level of Torah obligation. At first glance, then, it would appear improper to recite this text, given that the consensus among the halakhic authorities follows the majority view, that sefirat ha-omer is observed today on the level of Rabbinic enactment.
Indeed, Rav Ovadya Yosef, in Yechaveh Da’at (6:29), writes that those who recite this prayer should amend the text to reflect the accepted position. Specifically, Rav Ovadya writes that one should recite, “le-kayeim mitzvat sefirat ha-omer,” instead of “mitzvat asei shel sefirat ha-omer,” and omit the citation of the verse (that is, from “kemo she-katuv ba-Torah” until isheh le-Hashem”).
Rav Shlomo Zalman Auerbach, however, as noted in Halichot Shelomo (Moadim, Nissan-Av, p. 350), defended the accepted text of the “Hineni Mukhan U-mezuman” prayer. He claims that the term “mitzvat asei” does not necessarily refer to a Torah obligation, as it can also be used to describe an obligation enacted by Chazal. And as for the citation of the verse, Rav Shlomo Zalman maintained that this can easily be explained as referring to the fact that the Sages enacted a requirement to count the omer nowadays just as the Torah commands counting the omer in the times of the Mikdash. Therefore, in his view, there is no need to amend the text of this prayer to accommodate the majority view among the Rishonim.