President Shimon Peres on Thursday said Deputy Foreign Minister Danny Ayalon's treatment of the Turkish ambassador reflected the "mistake of one man, not of the state."
"It was not diplomatic... and it's good that he apologized," Peres said.
Israel sparked outrage on Monday when envoy Ahmet Oguz Celikkol, summoned by Ayalon over an anti-Israeli television show aired in Turkey, was made to sit in a chair lower than that of Ayalon, while the Turkish flag was deliberately not put on display.
Ayalon issued a formal apology to Ankara at Peres' request, and at the culmination of day-long consultations between Ankara and Jerusalem, made after the Turks announced that Ayalon's first apology was insufficient.
"This should not be connected to the whole state or to all diplomats," said the president. "We must learn not to do this again.
Foreign Ministry officials on Thursday slammed a group of 17 MKs who sent a letter of apology to Turkey over Ayalon's treatment of the ambassador.
"Ayalon respects the MKs who apologized, but where were they over the past two years of anti-Semitic broadcasts in the Turkish media and unbridled criticism of Israel from Ankara," one official told Israel Radio.
"After two years in which Turkey has failed to get the diplomatic message, we had to start making a noise," a member of Ayalon's staff said.
At the beginning of his Monday meeting with Celikkol, Ayalon told cameramen in Hebrew: "Pay attention that he is sitting in a lower chair ... that there is only an Israeli flag on the table and that we are not smiling."
In his own official letter of apology issued Wednesday evening, Ayalon wrote: "I had no intention to humiliate you personally and apologize for the way the demarche was handled and perceived."
"Please convey this to the Turkish people for whom we have great respect. I hope that both Israel and Turkey will seek diplomatic and courteous channels to convey messages as two allies should," Ayalon wrote.
Ayalon had sent an initial apology on Tuesday night, but Ankara had threatened to recall Celikkol if no second, formal apology was made.
According to Turkish media reports, this step had been taken, with Celikkol set to return Thursday morning after Israel said no such apology was on the table.
"My protest of the attacks against Israel in Turkey still stands," Ayalon said. "However, it is not my way to insult foreign ambassadors and in the future I will clarify my position by more acceptable diplomatic means."
Turkish Prime Minister Recep Tayyip Erdogan on Wednesday confirmed that Turkey had received the official apology from Israel over what the Turkish ambassador termed "humiliating" treatment by Israel's Deputy Foreign Minister, saying that it was "the expected and desired response."
Erdogan added more criticism of Israel, telling a news conference: "Israel must put itself in order and it must be more just and more on the side of peace in the region."
Foreign Minister Avigdor Lieberman on Wednesday said Israel doesn't want a confrontation with Turkey, but that it won't tolerate anti-Semitic remarks and incitement against Jews.
Lieberman said Israel respects Turkey and its people, and expects the same in return.
Netanyahu on Wednesday expressed satisfaction with Ayalon's apology. He said that the deputy foreign minister's protest was justified, but that he should have used acceptable diplomatic means to express his outrage.
The deliberate insult enraged Turkey and deepened the rift that has emerged over the past year between the Jewish state and its closest friend in the Muslim world.
Meanwhile, a leader article in Thursday's edition of Al-Quds Al-Arabi, an Arabic-language newspaper published in London, praised Turkey's stance in relations with Israel, commenting that Israel's government understood no language other than force.
Despite Israel's official apology and a Turkish declaration that the crisis is over, relations between the two countries have been damaged irreparably, the newspaper said, predicting that Turkey and Israel would never again be as close as they were before Recep Tayip Edogan, the Turkish prime minister, came to power.
Turkey is undergoing a strategic shift, the paper said. With the road to Europe barred, Erdogan's government is turning eastwards towards the Muslim world.
The Turkish ambassador and the Turkish government were furious at the humiliation. In a sharply worded ultimatum to Israel earlier Tuesday, Ankara demanded an apology for what it described as Ayalon's demeaning treatment of its ambassador.
Headlines in Turkish newspapers on Wednesday showed deep outrage over the incident.
"Insolence," blared the daily Vatan, and Cumhuriyet proclaimed, "Ties with Israel are breaking down."
"Vile conspiracy," railed the Sabah, while the pro-Islamic Yeni Safak newspaper fumed: "Despicable and immoral."
Sources in the Prime Minister's Bureau said Tuesday the decision to invite the Turkish ambassador for a reprimand by Ayalon was made together with Lieberman.
At the Prime Minister's Bureau, they noted that Netanyahu was not aware of the way the reprimand would be carried out, "but the minute it happened the prime minister [gave] the foreign minister his full backing."