In this photo provided by Turkish Prime Minister's Press Service, Hamas leader Halid Mashaal, right, is greeted by Turkey's Prime Minister Recep Tayyip Erdogan in Ankara, Turkey, Friday, March 16, 2012. AP/Yasin Bulbul While the government of Turkish Prime Minister Recep Tayyip Erdogan faces an extensive corruption investigation targeting his inner circle, the country's problems far exceed domestic graft.

Turkey is entangled in several shady endeavors that could eventually jeopardize its standing as a key U.S. and NATO ally.

"This is not just a Turkish underworld problem. This is a global illicit finance problem that intersects with rogue regimes and terrorist non-state actors," Dr. Jonathan Schanzer, a former terrorism finance analyst at the U.S. Department of the Treasury, told Business Insider.

Based on his experience tracking issues manifesting in Turkey in recent years, Schanzer detailed the six "massive red flags" of the larger scandal:

1) Last year Turkey was almost blacklisted by the Financial Action Task Force (FATF), an international terror finance regulatory body, for being out of compliance with its status obligations.

"It was remarkable not because they were out of compliance, but because they were out of compliance for seven years," Schanzer, who is now the vice president of research at the Foundation for Defense of Democracies, told BI. "They didn't do anything and they waited until the 11th hour to make changes."

The only countries currently blacklisted by the FATF are Iran and North Korea.

2) "Turkey appears to be a top sponsor of Hamas right now," Schanzer said, referring to the U.S.-designated terrorist group that governs the Gaza Strip. He cited material support flowing from Turkey to Hamas for the construction of schools and mosques as well as unconfirmed reports of $300 million in annual aid.

"If you take that and you add that to what we can now confirm of Hamas operatives working on Turkish soil, then there is an even greater cause for concern," Schanzer said. Multiple sources told Schanzer that Salah Al Arouri, the No.5 or 6 in the Hamas organization, is known to be based in Turkey.

Arouri founded the West Bank branch of the Qassam Brigades, which is the armed wing of Hamas. The group stood out in eight day war against Israel in November 2012 and continues sporadic rocket attacks against Israel.

"If one starts to connect the dots, you can't help but wonder if Arouri is directing these attacks from Ankara or wherever," Schanzer said, noting that other Hamas operatives may be active in Turkey. "If you think of their efforts to join the EU [and] their alliance with the U.S., it's just remarkable that they would take those sorts of risks" given U.S. laws against sponsoring terrorism.

3) Syria: "We continue to hear about the flow of weapons and goods and people over the border and the border is rather porous," Schanzer said. He noted that while "the Turks need to do this to maintain good relations to whomever is on the other side of the border," there are indications of assistance beyond lax border security.

In December the U.S. Treasury designated Abd al-Rahman al-Nuaymi, the Qatari head of a prominent Geneva-based human rights group, as a major al-Qaeda terrorist financier and facilitator in Syria (and elsewhere).

Nuaymi, who was contacted in Istanbul by the Financial Times, denied the charges.

"One just needs to put all of the things together to start to see a much more troubling trend," Schanzer told BI.

4) Erdogan's relationship with Yasin al-Qadi, a Saudi billionaire who was listed as a "Specially Designated Global Terrorist" by the U.S. Treasury in October 2001 for allegedly funding Osama bin Laden, Hamas, and other terrorist groups.

"The interesting thing about the al-Qadi issue is that when he was first designated, his front companies were all based in Turkey ... and he had quite a bit of operations on Turkish soil," Schanzer told BI.

Erdogan has defended al Qadi for more than a decade. The prime minister's security detail has also escorted al Qadi into Turkey without a passport or visa. A list of people due to be arrested in the corruption probe included al Qadi, who is reportedly linked to the prime minister's son Bilal, but the orders were not carried out.

"We don't know exactly what the relationship is with al-Qadi, but we know that his problems started in Turkey," Schanzer said. "It's very hard to look at this right now without remembering that and asking the question: Has he remained active in Turkey through this time?"

5) An extensive gas-for-gold scheme involving Iran, which ran from about March 2012 to the fall of 2013 and yielded Iran more than $13 billion dollars amid crippling sanctions implemented by the U.S. over the country's perceived nuclear program.

"It's a huge amount of money," Schanzer, who recently detailed the arrangement in Foreign Policy, said. "You can't ignore the fact that the Turks helped Iran with a massive sanctions-busting scheme."

6) "To add insult to injury, we have the Chinese missile deal ... where the Turks contracted with a Chinese company that's already on [the U.S.] proliferation list."

So while the domestic corruption issues and political battle between Erdogan and powerful Islamic network created by Fethullah Gulen will be decided through courts and elections, the reasons listed above are international and central to U.S. interests in the region.

Resolving these issues — particular those involving Erdogan's government supporting two suspected al Qaeda financiers and a U.S.-designated terrorist organization — may be critical to a continued alliance between Turkey and the U.S.

"Yes it will be a sensitive issue and yes it will raise issues with Washington, but the alternative is unthinkable," according to Schanzer. U.S. President Barack Obama and Turkish Prime Minister Tayyip Erdogan (L) meet in New York September 20, 2011. REUTERS/Kevin Lamarque That alternative would involve the status quo continuing to the point where members of Congress or the State Department or the Treasury were forced consider labeling Turkey a state sponsor of terrorism.

"No one wants to do that, but the letter of the law is getter harder and harder to ignore that they might qualify," Schanzer said. "If left unchecked, this could be become a serious problem."

The obstacle for the U.S. is that, given the Obama administration's divergent Middle East policy, Washington hasn't put itself in the best position to influence Erdogan's government.

"One gets the sense that the wheels started to come off across the board: Our Syria policy didn't hold up; our Iran policy appears to be at odds with itself; and our general counterterrorism policies across the region don't seem to be applied consistently," Schanzer said. "Turkey seems to be in the middle of all of that."