Israel's ambassador to the UN Dan Gillerman denounced Thursday's statement, issued while Annan was in Brussels, which made no mention of the attack on a bus or the 10 Israelis killed.
He said that Annan may not have even seen the statement issued in his name, a claim rejected by a UN spokeswoman.
"No mention is made of Israeli victims slaughtered in the bombing... no specific reference is made to the attack at all," Gillerman said on Friday.
"The moral clarity of the secretary general in expressly condemning brutal acts of terrorism like yesterday's attack is especially important.
This is why we must unfortunately express our disappointment and dismay."
Annan's statement issued after the attack, which also wounded around 50 people, said: "Once again violence and terror have claimed innocent lives in the Middle East. Once again I condemn those who resort to such methods.
"Once again I appeal, to Israelis and Palestinians alike, to rise above feelings of anger and vengeance, and to devote all their energies to negotiating a true and lasting peace in which two peoples will live side by side, each in their own state"
UN Secretary General
"Once again I appeal, to Israelis and Palestinians alike, to rise above feelings of anger and vengeance, however natural, and to devote all their energies to negotiating a true and lasting peace in which two peoples will live side by side, each in their own state."
Annan also said that he had always condemned bombings "without reservation".
Annan's spokeswoman Marie Okabe rejected Gillerman's claim that her boss did not read the statement, as well as any suggestion that it represented a shift in his attitude toward the Israeli-Palestinian conflict.
"There has been no change," she said. "The secretary general has consistently and strongly condemned all acts of terrorism from whatever quarter, including the bombing in Israel yesterday."
She added: "The secretary general does see and read and sign off on everything."
Respect for Annan
However, Gillerman repeatedly said he had great respect for Annan and underlined that Israel has usually drawn a distinction between the UN's political organs and the secretariat under Annan.
Gillerman has reiterated Israel's
respect for Annan
But, saying his country faces bias "that borders on the absurd," he added that in light of the UN's role as a co-sponsor of the roadmap plan for Middle East peace, Israel's treatment at the world body was "too troubling to pass without comment".
Gillerman was also upset over political developments on Thursday, when the Security Council failed to agree on a statement about the bombing because of opposition from Algeria.
Algeria and others wanted any statement to make reference to the eight Palestinians killed the day before the attack in a raid by Israeli forces, diplomats said.
"To focus on the response to terrorism and not on the terrorism itself is unfair and harmful to the cause of peace," said Gillerman.
Israel has long complained about its treatment by the world body, whose general assembly regularly passes measures condemning its treatment of the Palestinians.
The assembly has also asked for a ruling from the International Court of Justice in The Hague on whether the separation barrier Israel is building in the West Bank is legal.
With hearings set to begin on 23 February, Israel on Friday formally challenged the court's competence to rule on the barrier.