The Torah introduces the obligation of Sefirat Ha'omer in the Book of Vayikra (21:15): "You shall count for yourselves from the day following the Shabbat, from the day when you bring the Omer that is waived – they shall be seven complete weeks." The Sages explained that "the day following the Shabbat" refers to the day following the first day of Pesach, or the sixteenth of Nissan, the second day of Pesach. On that day we begin counting and continue each day for seven weeks (forty-nine days).
The Shibolei Ha'leket (Halachic work by Rabbi Tzidkiya Ben Avraham, Italy, 1230-1300) cites (in Siman 236) a passage from the Midrash which tells that when Benei Yisrael left Egypt, Moshe informed them that in fifty days they would be receiving God's Torah. Moshe had learned this information when God first spoke to him at the burning bush, when He declared, "When you take the nation from Egypt, you shall serve God on this mountain" (Shemot 3:12). The word "Ta'avdun" ("you shall serve") is written with a seemingly superfluous letter "Nun," which has the numerical value of fifty. God thereby alluded to Moshe that fifty days after Benei Yisrael's departure from Egypt they would come to that mountain – Mount Sinai – to receive the Torah. Benei Yisrael reacted to this information with great enthusiasm, and counted each day after the Exodus in eager anticipation of the receiving of the Torah. God therefore commanded that we commemorate their enthusiasm by counting the days each year from the day following the Exodus until the festival of Shavuot, which celebrates the giving of the Torah.
According to the majority of Halachic authorities, including the Shulchan Aruch (489), the obligation of Sefirat Ha'omer applies nowadays only on the level of Rabbinic enactment. Since the Torah linked this counting to the Omer offering brought on the sixteenth of Nissan ("You shall count…from the day when you bring the Omer"), the Biblical obligation applied only when the Temple stood and the Omer offering was brought. In the absence of the Beit Ha'mikdash, the Torah obligation no longer applies, and we are required to count the Omer only on the level of Rabbinic enactment.
This point is of great importance with regard to the "Le'shem Yichud" introduction that many people have the practice to recite before counting the Omer. This paragraph speaks of the counting as a "Mitzvat Asei" – an affirmative command from the Torah. In truth, however, as mentioned, we do not count the Omer nowadays in fulfillment of the Biblical command, and it is therefore improper to refer to the counting as a "Mitzvat Asei." It should be noted that according to the Rambam (Rabbi Moshe Maimonides, Spain-Egypt, 1135-1204), in Hilchot Mamrim (2:9), if a person claims that eating chicken with milk constitutes a Torah violation, he transgresses the prohibition of "Bal Tosif" – adding onto the Torah. Since eating chicken with milk is permissible according to Torah law, and was forbidden only by the Sages, referring to this law as a Biblical prohibition amounts to adding onto the Torah's laws. Similarly, Chacham Ovadia Yosef rules (in Chazon Ovadia – Laws of Yom Tov, 214) that one who recites the "Le'shem Yichud" before counting the Omer must omit the reference to the counting as a "Mitzvat Asei," lest he be in violation of "Bal Tosif." Furthermore, he adds (ibid. p. 115), on the final night of Sefirat Ha'omer, one must not recite in the "Le'shem Yichud" the verse which makes reference to the seven weeks of counting "Sheva Shabatot". By making such a reference, one thereby fulfills his obligation to count that night and may then no longer count with a Beracha. One who recites the "Le'shem Yichud" before counting on the final night should therefore omit this reference.
Summary: The obligation to count the Omer applies nowadays only on the level of Rabbinic enactment, and therefore one who recites the "Le'shem Yichud" introduction before counting must omit the words "Mitzvat Asei Shel Sefirat Ha'omer," which refers to the counting as a Biblical command. On the final night of the Omer, one must also omit from the "Le'shem Yichud" the part of the verse that makes reference to "seven complete weeks."