U.S. authorities would not release Pollard, who is jailed for spying for Israel, from federal prison in North Carolina for Monday's funeral for Morris Pollard, 95, a prominent U.S. researcher on viral diseases who died June 18 of complications from a bladder infection.
The funeral was held at a Jewish cemetery in South Bend, Ind.
Pollard supporters had shut down the White House switchboard after flooding it with calls urging his release to attend the funeral.
Israel had officially requested that the Obama administration let Pollard leave prison for a brief compassionate release to pay his respects at the funeral.
The Conference of Presidents of Major American Jewish Organizations in a news release Monday expressed regret that Pollard was not allowed to attend the funeral.
"We believe that this humanitarian gesture was warranted," wrote Richard Stone and Malcolm Hoenlein, the chairman and executive vice chairman, respectively, of the umbrella group. "It underscores the need for prompt action to release Jonathan Pollard after 25 years of imprisonment."
At least 200 supporters of Pollard, a civilian analyst for the U.S. Navy when he was convicted of spying for Israel, had demonstrated Sunday in front of the U.S. Embassy in Tel Aviv, urging Obama to accede to the request.
More than 70 Knesset members last week sent a petition to Washington urging Obama to allow Pollard to visit his dying father. Activists and organizations from around the world, including the Conference of Presidents of Major American Jewish Organizations, had urged Obama to grant Pollard the compassionate leave, but the administration refused.
Pollard, who was arrested in 1985 and is serving a life sentence, was allowed to make an emergency call to his hospitalized father a week before his death, but Morris Pollard was too weak to speak on the telephone.
Pollard was not allowed to attend his mother's funeral in December 2001. He reportedly has been estranged from his family since 1996.