The union's pro-Palestinian stance is expected to be debated in Torquay this weekend, when it holds it annual conference.
But the Board of Deputies of British Jews says the issue is divisive and should not be on the agenda. It does not accuse NATFHE of being racist but says its position could fuel anti-semitism.
"It is the duty of lecturers to present balance in the classroom," said Fiona MacAulay, public affairs chief at the board. "Many of NATFHE's statements are not necessarily anti-semitic, but the demonising of Israel has the effect of smearing British Jews."
Paul Mackney, NATFHE's general secretary, says the union has had several letters from Jews about its position on the Middle East, the majority of them in support of its stance, and written by Jews who are themselves critical of Israel.
The union says it was contacted by the Israeli Embassy and has agreed to distribute material putting the country's case on the Palestinian question.
A spokeswoman for the union said: "The position NATFHE is taking is not against the Jewish people. It is against the state of Israel."
As The TES went to press, it remained unclear when any discussion about the Middle East would take place, although it is understood that Monday is favoured, partly to make sure people who observe the Jewish Sabbath are able to attend.
Last month, NATFHE issued a statement opposing the "barbaric incursion of the Israeli Defence Force into areas under the jurisdiction of the Palestinian authority, including Palestinian universities and colleges, which has led to the death and injury of several hundred Palestinian civilians."
NATFHE has called on British academic institutions to re-consider their links with Israel. It has called on Israel to withdraw from areas which officially fall under the Palestinian authority's control.
It also urged Israel to lift its siege on the headquarters of the Palestinian leader Yasser Arafat.