This time, however, many Turks have been expressing their dissatisfaction with these links, particularly over troubled weapons programmes.
With millions of dollars invested in upgrade projects for Turkey's ageing tank and warplane fleets, an apparent lack of delivery by the Israelis has left many questioning just how - and why - these procurement deals were made.
The trouble began in the late 1990s and early 2000s, when Turkey signed up to deals allowing Israeli Military Industries (IMI) to upgrade US-built F-4E warplanes and M-60A1 tanks.
Now, years later, the F-4 upgrade is still incomplete - while some of those delivered have crashed. At the same time, Israel was due to hold test firing trials for the M-60s last summer, but still has not overcome a range of technical problems - leaving the tanks still in the workshop.
"The complaint here is that Israel isn't meeting its contract commitments," says senior Ankara-based defence analyst Lale Sariibrahimoglu. "Many question marks have therefore been raised about the Israelis."
Last month, Turkey's defence procurement panel, the Defence Industry Executive Committee, suspended a $93 million payment due to IMI over the delays on the M-60 project. The total cost of the upgrade was initially budgeted at $688 million for 170 tanks - although sector insiders suggest that with delays the cost now may be in excess of $1 billion.
"If you do the maths, this makes the M-60s the most expensive tanks in the world," adds Sariibrahimoglu.
An Israeli US-made M-60 tank
in the West Bank
"The tanks are old - it's like trying to turn a 50-year-old lady into a 25-year-old girl."
Sector insiders complain that the upgrade makes the M-60s cost about $4 million each - more expensive than brand-new Ukrainian or Russian T-84 tanks, which weigh in at about $3 million each.
Meanwhile, Turkish defence industry executives are also concerned over Turkish military plans to give a further upgrade contract to the Israelis for another batch of 48 F-4Es. The Israelis had already upgraded a first consignment of 54 of these, delivering them only after a number of other problems.
The undersecretariat for the Defence Industry argues that this further upgrade can be done in Turkey with only an advisory role for Israeli technicians. Yet the Turkish Air Force is adamant that the upgrade should be done by IMI in Israel - despite previous problems.
Two of the original batch of F-4s crashed last year on a routine flight. "The air force stated that these were not the result of technical failures," says Sariibrahimoglu. "Without any public inquiry into the crashes, we can only speculate if there were other reasons."
And this raises one of the key questions now enveloping the whole Israeli arms issue. Many Turkish defence analysts and industry insiders say that a lack of transparency surrounds the whole procurement issue.
This questioning comes at a sensitive time too, as the issue of military commanders accepting large, undisclosed commissions has recently been raised by the trial of retired Admiral Ilhami Erdil, who commanded the Turkish navy from 1999 to 2002. He has been accused of major irregularities in the awarding of military contracts.
A Turkish vessel in manoeuvres
with the US and Israel
It has also come at a time when Turkey's relationship with Israel - much touted by Tel Aviv - has been going through a reappraisal in Ankara.
"The Turkish government has adopted a new foreign policy towards the Middle East and is prioritising good relations and stability with all its neighbours," says Assistant Professor Bulent Aras of Istanbul's Fatih University International Relations Department.
"Given the actions of the Sharon regime, Israel has therefore emerged as a very problematic country for Turkey."
In the late 1990s, Turkey and Israel cooperated closely on a range of security issues - from joint naval manoeuvres with the US to pressuring Syria to force out Kurdish rebel leader Abdullah Ocalan, who was based in Damascus. Meanwhile, trade has flourished.
Yet, with the election of the Justice and Development Party (AKP) government in late 2002, things changed.
Erdogan accuses Israel of
practicing state terrorism
Prime Minister Recip Tayyip Erdogan has accused Israel of conducting state terrorism against the Palestinians, while the party's emphasis on improving relations with the Arab world has cut up against the country's Israeli ties. Ankara has also been through a period of more distant relations with the US -the major sponsor of Israeli-Turkish friendship.
However, "While with the AKP, relations with Israel have been souring in general, it has been business as usual for the military," says Sariibrahimoglu.
Part of the reasoning is that Turkey's commanders want the latest weapons technology to be transferred to Turkey. The US and Germany have both refused to do this in recent years, but Israel - which receives much leading edge equipment from the US - came forward as a back channel for these transfers.
Yet, as one senior defence industry insider told Aljazeera.net on condition of anonymity: "The Israelis said they would transfer new weapons technology, yet none of this has come. This has created a major problem."
Against this background, Israeli Army Chief of Staff Moshe Yaalon flew to Ankara on 1 February for consultations with Turkish military officials. The F-4 and M-60 upgrades were likely high on the list of topics, as was Turkish procurement of Harpy-2 drones, pilotless warplanes, from Israel.
The talks are likely to have been heated.