The comments come as a rebuke to US President George W. Bush who described it as a "problem" in landmark talks with Palestinian prime minister Mahmud Abbas at the White House.
"The building of this security fence has no political connotations. It's a necessity dictated by the security imperative of preventing Palestinian suicide bombings against Israel," the official told the AFP news agency, asking not to be named.
Speaking at a joint press appearance with Abbas on Friday in the White House Rose Garden, Bush rold reporters, "I think the wall is a problem, and I have discussed this with (Israeli Prime Minister) Ariel Sharon.
"It is very difficult to develop confidence between the Palestinians and the Israelis ... with a wall snaking through the West Bank."
Israel has admitted a rift is emerging with Washington over the issue, but says the wall, which could eventually meander up to 900 km (550 miles), will prevent the infiltration of resistance fighters from the West Bank.
Bush, wading ever deeper into Middle East peacemaking after giving it a wide berth during the first two years of his administration, is due to meet Sharon next week at the White House.