Former U.S. Secretary of State Hillary Clinton greets guests before U.S. President Barack Obama awarded former U.S. President Bill Clinton the Presidential Medal of Freedom in the East Room at the White House on November 20, 2013 in Washington, DC. The Presidential Medal of Freedom is the nation's highest civilian honor, presented to individuals who have made meritorious contributions to the security or national interests of the United States, to world peace, or to cultural or other significant public or private endeavors. Win McNamee/Getty The Clinton Foundation's finance controversies deepened on Thursday, when The Boston Globe reported that a huge affiliate of the charity failed to report its foreign-government contributions to the State Department.

When Hillary Clinton, now the leading Democratic presidential candidate, became secretary of state in 2009, she agreed to have her family's foundation submit new donations from foreign countries for State Department review. This was designed to avoid potential conflicts of interest with her new government role.

But Clinton's foundation, now called the Bill, Hillary & Chelsea Clinton Foundation, and its various initiatives repeatedly violated this agreement, reports over the past few months have shown. The Washington Post reported in February that the Clinton Foundation failed to disclose $500,000 from Algeria at the time the country was lobbying the State Department over human-rights issues. And Bloomberg reported this week that the Clinton Giustra Enterprise Partnership, a Clinton Foundation affiliate, failed to disclose 1,100 foreign contributions.

And The Globe's report on the Clinton Health Access Initiative (CHAI), another foundation affiliate, may cover the most notable omissions yet as tens of millions of dollars went undisclosed to the State Department.

"Government grants to CHAI, nearly all of them from foreign countries, doubled from $26.7 million in 2010 to $55.9 million in 2013, according to the charity's tax forms," The Globe reported.

According to the paper, CHAI "makes up nearly 60% of the broader Clinton charitable empire" and has an annual budget of more than $100 million.

"The failures make the Clinton Health Access Initiative ... a prominent symbol of the broken political promise and subsequent lack of accountability underlying the charity-related controversies that are dogging Clinton as she embarks on her campaign for president," The Globe's Annie Linskey wrote.

Clinton before delivering the keynote address at the Women in the World summit in New York last Thursday. REUTERS/Shannon Stapleton

CHAI spokeswoman Maura Daley told The Globe that her organization "didn't think" it needed to report many of the contributions because they were simply increased payments from existing donor countries.

The "memorandum of understanding" the Clinton Foundation reached with the White House, however, indicates otherwise under CHAI's section of the agreement:

Should an existing contributing country elect to increase materially its commitment, or should a new contributor country elect to support CHAI, the Foundation will share such countries and the circumstances of the anticipated contribution with the State Department designated agency ethics official for review.

Indeed, a spokesman for Secretary of State John Kerry said CHAI should have disclosed the contributions.

"We would have expected that CHAI identify for the department the foreign-country donors that elected to materially increase their donations and new country donors. The State Department believes that transparency is the critical element of that agreement," the spokesman, Alec Gerlach, told The Globe.

Additionally, the paper reported that CHAI failed to disclose numerous payments from new donor countries, which Daley had various explanations for. Switzerland was an "oversight." Rwanda's $300,000 was considered a "fee" rather than a contribution. And CHAI did not consider Flanders a "foreign government" because it is part of Belgium rather than an independent country.

The agreement the Clinton Foundation struck with the White House, however, said CHAI contributions should be considered "a foreign country" if they are from "an agency or department of a foreign country, as well as a government-owned corporation."

Former President Bill Clinton. Reuters//Brendan McDermid

When previously confronted with criticism of the foundation, the Clintons and their allies have pointed to their nonprofits' beneficial projects around the world. CHAI, for example, began as the Clinton HIV/AIDS Initiative and seeks to achieve "a large-scale, transformation, and lasting impact that saves and improves people's lives," especially in the developing world.

But in the world of 2016 campaign politics, the reported $2 billion Clinton Foundation has proved to be a repeated headache for both Hillary Clinton and her family's charity network.

Last week, The New York Times connected the foundation's contributions to the sale of US uranium production to Russia. The Washington Post noted that Bill Clinton was paid $26 million in speaking fees from the foundation's major donors. And Reuters revealed the foundation's tax returns misreported tens of millions of dollars from foreign governments.

Politico's Ken Vogel reported Thursday that the charity was in a "campaign tailspin" as the former secretary of state seeks the White House.

"The uncertainty comes at the beginning of what was supposed to have been a four-month victory lap," Vogel wrote. "Instead, it's turned into heartburn for Hillary Clinton's campaign for the Democratic presidential nomination and for the foundation, which has been under increasing pressure to distance itself from its more controversial partners."