The flotilla incident - in which eight Turkish citizens and a US citizen of Turkish descent were killed by Israeli commandos - brought already worsening relations between the countries to a low point.
Though it included activists representing six international NGOs, the mission was primarily organized by the Foundation for Human Rights and Freedom and Humanitarian Relief (IHH), a Turkey-based charity.
Since the flotilla episode, Turkish-Israeli relations have been 'worse by far, with no prospect of improvement any time soon,' Semih Idiz, a political analyst and columnist for the Turkish daily Milliyet, told the German press agency dpa.
'The two sides are very entrenched. Each side has its own reasons, especially from the Turkish perspective,' he said.
Relations between Turkey and Israel, once close allies in a turbulent region, had begun to sour in recent years, as Turkey began to assert itself as a more active player in the Middle East.
Turkey showed an increased willingness to criticize Israel's policies toward the Palestinians.
Israel's incursion into Gaza at the end of 2008 was seen by Turkey as an unjustifiable act of aggression.
Turkish Prime Minister Recep Tayyip Erdogan made this clear by storming off the stage at a discussion with Israeli President Shimon Peres at the World Economic Forum in Davos, Switzerland in January 2009.
The flotilla incident was the final straw for Turkey, which withdrew its ambassador to Tel Aviv and demanded that Israel apologize and pay compensation to the victims' families.
Israel has rejected the demands, saying the commando assault on the Mavi Marmara, the largest ship in the flotilla, was carried out in self-defence.
Offering compensation would amount to an admission of fault that could lead to legal cases against its armed forces.
In December, hopes for rapprochement were briefly raised when Turkey sent two planes to Israel to help fight a forest fire - the country's worst ever - on Carmel Hill.
Not long after, Turkish and Israeli officials met in Geneva in the first bilateral encounter in nearly six months.
But the crisis in relations has continued, with both sides apparently unwilling to back down and as politicians in both countries play to domestic public opinion.
Turkey's ruling Justice and Development Party (AKP) government is expected to be re-elected in parliamentary elections set for June 12.
In the meantime, a United Nations panel of inquiry, chaired by legal expert Sir Geoffrey Palmer, recently further postponed releasing its report on the issue, apparently due to a lack of consensus on the panel, which includes one Turkish and one Israeli member.
'There's a total disconnect. There is no common understanding as to what the mandate of that [panel] is. The Americans see it as a 'kiss and make up' commission; the Turks expect it to say Israel is the guilty party,' Idiz said.
The 'Freedom Flotilla II-Stay Human II,' a second flotilla that the IHH and 21 other groups have announced they will send to Gaza in late June, is likely to further exacerbate relations.
In response to attempts by the United States and United Nations to discourage Turkey from allowing the mission to take place, Ankara has insisted that democratic countries cannot control the actions of NGOs.
'It is firstly Israel that should be warned, that the crime committed last year has still not been accounted for,' Turkish Foreign Minister Ahmet Davutoglu said in an interview last week with Radikal newspaper.
Some observers, who point out that Egypt's recent decision to open the Rafah crossing between Gaza and Israel allows residents of Gaza to obtain most of the goods they need, allege the planned flotilla is a provocation.
'At the end of the day, what [the IHH] are doing is politics; this is a political mission,' Mensur Akgun, director of the Global Political Trends Center at Istanbul Kultur University, told dpa.
Yet despite ongoing political tensions, economic ties between Turkey and Israel have remained strong.
Bilateral trade increased by 40 per cent in the first quarter of 2011 year-on-year, and Turkey is Israel's biggest trading partner in the region, Turkish daily Hurriyet Daily News reported Monday.
Considering not only economics but also the two countries' longstanding historical relationship, Akgun said it was in their best long-term interest to work on mending fences.
'It's not in the interest of Turkey or of Israel to have bad relations between the two countries,' Akgun said.
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