Yahia Youssef Yaish is being interrogated by the intelligence service run by Shi'ite Houthi rebels, who control the country's capital, Sanaa, the officials said on Tuesday.
Three airport employees have also been detained over the same allegations, the added, speaking on condition of anonymity because they are not authorized to speak to the media.
In Israel, Avi Mayer, the spokesman for the Jewish Agency, confirmed the Torah scroll was smuggled out of Yemen with a rabbi and 18 Yemenite Jews who left to Israel last month.
Yemeni intellectuals issued a statement demanding Yaish's release and describing allegations against him as "fabricated."
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