The Obama Administration is scrambling to keep itself out of a difficult position between two of its most important Middle East allies, Turkey and Israel.

The two countries have seen their relations deteriorate for years now, highlighted by Turkish Prime Minister Recep Erdogan’s dressing down of Israeli President Shimon Peres at the World Economic Forum in 2009 and the confrontation over Israel’s killing of nine Turks on the Mavi Marmara, a ship trying to run the blockade of Gaza last year.

Analysts have a variety of opinions on the importance of each country to US interests in the region, but US diplomats certainly want to keep a strong relationship with both. Congress, pushed by domestic pressures, especially pro-Israel lobbying groups, has a different approach.

The potential for problems for US diplomacy was previewed in March, 2010. The House Foreign Affairs Committee, which had always been reserved on the matter of the Armenian Genocide (perpetrated by the Turks during and after World War I) issued a statement calling for American recognition of that crime. Turkey recalled its ambassador in response.

The matter went no further, but it illustrated the tensions between politics and diplomacy.

The pro-Israel lobby promoted the Armenian Genocide resolution. Now, however, they are supporting Netanyahu and potential rapprochement between Turkey and Israel. But that resolution was a signal that this could change, if Turkey’s relations with Israel degenerate further.

Israel and Turkey are at odds, but still technically allied. The Obama Administration wants to mend those fences, not tear them further asunder.

The immediate issue is Turkey’s demand for an apology for the Mavi Marmara killings. The UN will soon release a UN report, delayed now until August 20, which will state that Israel’s blockade in Gaza is legal, but that it used excessive force on the Mavi Marmara. If Israel apologizes before that report is released, it will blunt the effect of the latter conclusion.

Indications are that Israeli Prime Minister Benjamin Netanyahu is willing to issue some kind of apology, though doubtless it will be worded in such a way that Israel can continue to paint it as an unfortunate incident and that it was not really at fault. Such an apology could well be enough.

But Netanyahu, who has considerable support in his cabinet for this course, is concerned by the staunch opposition to it from his Foreign Ministry, which is in the hands of the radical right-wing party, Yisrael Beiteinu.

Foreign Minister Avigdor Lieberman and his deputy, Danny Ayalon have repeatedly tried to poison this relationship, well before the Mavi Marmara incident. This has never sat well either with the Prime Minister or in DC.

Lieberman has already blasted Netanyahu for even considering an apology to Turkey, despite the importance of that relationship to both Israel and the US. This is a continuation of Lieberman’s campaign to sunder the relationship with Turkey. He’s also using this to punish Netanyahu for his work against Yisrael Beiteinu’s anti-NGO bill last week.

The Israeli far right has been increasingly hostile toward Turkey ever since the current government came to power. They are generally opposed to anything that places diplomatic constraints on Israeli actions, which friendship with a Muslim state inevitably does.

That mistrust grew by leaps and bounds after Erdogan’s tirade against the occupation at Davos in ‘09. Turkey is also working to increase its leadership role in the region and to find a way to defuse the tensions between Iran and the West. All of this frightens the right and one suspects this is why the Foreign Ministry has worked to sour Israeli relations with Turkey.

Netanyahu, as well as key aides such as Defense Minister Ehud Barak and Deputy Prime Minister Dan Meridor, agrees with Obama that it is better to mend the relationship than let the split fester or worsen. But Lieberman can, potentially, bring down the Israeli government, and few in Israel really believe that they have anything to apologize for over the Mavi Marmara incident.

The UN decision to delay the release of the report was probably something the US, Israel and Turkey all agreed should happen. Obama, Erdogan and Netanyahu all want to work toward finding a way for Israel and Turkey to come to terms.

But will Lieberman let them?

For the US, it brings up a nightmare scenario. While the pro-Israel lobby supports Netanyahu’s desires, if Lieberman wins this tug of war, it will mean that Netanyahu’s public stance will change, and so, quite likely, will the lobby’s behavior.

A Congress hostile to Turkey will have plenty of fodder. Turkey wishes to maintain good relations with Syria and Iran, which can be a valuable asset for a US government that doesn’t often find it easy to talk to those two countries. But the potential for anti-Turkey propaganda there is obvious, and last year’s incident was an example of how easily, and disastrously, this situation can turn.

It will be very difficult for Obama Administration, or any other, to ignore that sort of force and pursue the US’ obvious interest in a strong relationship with Turkey.

They really can’t afford to let the dispute on this issue between Netanyahu and Lieberman remain an internal Israeli issue, mostly because the lobby will ensure it impacts US policy. The Administration seems to appreciate this. They’ll have to hope their effort pays dividends, or the price for the “special relationship” with Israel could escalate quite sharply.