The Israeli government sent a lower-level diplomat from its consulate in Istanbul, rather than a senior official.
Gul said the near-unanimous condemnation showed Israel was isolated and that it "will suffer the consequences for its mistake against Turkey."
Many of the passengers on board the flotilla were Turkish, including nine people who were killed.
The presidents Mahmoud Ahmadinejad of Iran, Bashar al-Assad of Syria, Hamid Karzai of Afghanistan as well as Russian Prime Minister Vladimir Putin and Palestinian leader Mahmud Abbas were among the leaders who attended the security summit.
Putin said Russia would raise at the UN the controversial issue of who should investigate the Israeli raid, which he denounced as "a crude violation" of international law.
"We can't allow a new flame to flare up in the Middle East.... We will raise the issue at the United Nations, we're working at it," he told reporters.
The Israeli government pledged to launch its own investigations into last week's deadly raid, after rejecting a UN proposal for an international probe into the attack.
In a statement on Monday, the Israeli military said it was gathering an "internal team of experts" to examine the operation and "establish lessons from the event".
It said the investigation would report its findings on the attack, which left nine activists dead and more than 100 wounded, on July 4.
|Turks have been outraged by the Israeli raid
on the aid flotilla [Reuters]
The Israeli government is also set to announce its own investigative panel, defence minister Ehud Barak told Israel's parliament on Monday.
Barak gave no details of the format of such a probe, which Israeli media reports said was still being worked out.
He also suggested Israel was also looking at ways to amend its four-year blockade on the Gaza Strip, although he added it would maintain restrictions it sees as essential to preventing Iranian missiles from reaching the Palestinian territory.
Barak said the planned investigation would run separately from the military investigation, and would seek to establish whether Israel's blockade of Gaza and its raid "met with the standards of international law".
"We will draw lessons at the political level, (and) in the security establishment," he said.
But many countries have demanded more, arguing that Israel cannot conduct an impartial investigation. Bashar al-Assad, the Syrian president, called on Monday for an international investigation and urged an end to the Israeli blockade of Gaza, which began in 2007.
"As a minimum we should see the establishment of a neutral investigation committee in addition to lifting the blockade," al-Assad said.
"If blood was shed for a certain objective we should make everything possible to achieve their objective [to break the blockade] and we should continue in our efforts on this path."
Anita McNaught, Al Jazeera's correspondent in Istanbul, said the Turkish government is looking for partners in the region to take action against Israel.
"What this regional security summit is about is Turkey figuring out what partners it has if it moves to try and isolate Israel, politically, economically, militarily, however it can," she said.
Turkey had a solid alliance with Israel until the Gaza war in early 2009.
Following last week's attack, Ankara said it would reduce its military and trade ties with Israel and has shelved discussions on energy projects, including natural gas and fresh water shipments.
It has also threatened to break ties unless Israel apologises for the raid.
Speaking on the sidelines of the conference, Ahmet Davutoglu, Turkey's foreign minister, said his country was "evaluating everything".
"It is up to Israel how our ties will continue," he said. "Israel has to accept the consequences of its actions and be held accountable".