In April of last year, Vice President Joe Biden called for a Senate Intelligence Committee report on CIA interrogation and detention programs to be declassified. More than two months later, The Daily Beast has learned, the State Department told Congress in a classified letter that declassifying the report could endanger American lives abroad and harm relations with foreign countries.

In other words, the Obama administration has been sending mixed signals on the release of the so-called “torture report” for nearly a year. (On Friday, the White House said it would like to declassify portions of the 6,300-page document.)

On Thursday, the Senate Intelligence Committee voted 11-3 to recommend declassifying the summary and conclusion of the report on Bush-era CIA detention and interrogation programs, prepared by their Democratic staff. Their investigation set off a public battle between the CIA and the Committee’s Chairwoman, Dianne Feinstein, who has accused the CIA of spying on the Committee’s investigation. The CIA will now be involved in reviewing and redacting any portions of the report that will be made public.

Two Republican senators who voted against declassification, Marco Rubio and James Risch, issued a statement after the vote revealing they had been warned by the State Department that declassification was not only an intelligence risk but also a threat to U.S. conduct of foreign policy.

“The Senate Intelligence Committee today voted to send a one-sided, partisan report to the CIA and White House for declassification despite warnings from the State Department and our allies indicating that declassification of this report could endanger the lives of American diplomats and citizens overseas and jeopardize U.S. relations with other countries. Therefore, we could not support declassification of this product at this time,” they said.

A senior Senate aide told The Daily Beast that the Rubio-Risch statement referred to a June 2013 classified letter to senators signed by Philip Goldberg, who at the time served as the State Department’s top intelligence official. The warning was in reference to the fact that the report contains information about cooperation with foreign intelligence agencies and the existence of still-undisclosed CIA “black site” prisons in foreign countries where abuses may have occurred. The letter warned of risks if proper security precautions were not taken.

CIA facilities implicated in the report have allegedly been located in Thailand, Poland, Lithuania, and Romania, sparking public debate and resentment against the U.S. government in those countries. But officials and senate aides said the report contains information on several more locations.

Diplomats representing those countries, aware of their vulnerability to exposure, have been quietly meeting with administration officials and lawmakers urging them to protect the secrecy of those intelligence relationships. Many foreign governments are still angry about the disclosures of NSA spying by leaker Edward Snowden.

“Embassies are concerned about their ability to contain the damage this release could do to their ability to work with the U.S.,” a senior Senate aide said. “European countries already have a problem with America spying on them, so something like this furthers the idea you can’t work the U.S. in a clandestine manner without it being splashed in the newspapers at some point.”

A senior administration official told The Daily Beast Friday that the letter was never cleared through State Department’s leadership and was never reviewed by the Secretary’s office or by the Under Secretary of State for Political Affairs. The warning came two months after Vice President Joe Biden publicly came out in support of declassifying the committee’s report.

“I think the only way you excise the demons is you acknowledge, you acknowledge exactly what happened straightforward,” Biden said. “The single best thing that ever happened to Germany were the war crimes tribunals, because it forced Germany to come to its milk about what in fact has happened.”

President Obama came out in support of limited declassification last month, after the feud between Feinstein and the CIA became public. Today, National Security Council Spokeswoman Caitlin Hayden declined to comment on the State Department’s letter.

“Having prohibited these practices upon taking office, the President believes that bringing this program into the light will help the American people understand what happened in the past and can help guide us as we move forward, so that no Administration contemplates such a program in the future,” she said. “Our position remains that the executive summary and the findings and conclusions of the final RDI [rendition, detention, and interrogation] report should be declassified, with any appropriate redactions necessary to protect national security.”

The State Department declined to comment on the Goldberg letter or the Rubio-Risch statement. Experts said that the State Department, unlike the White House or other elements of the intelligence community, has to deal with the fallout that some disclosures could have in foreign countries.

“The communication from INR is unusual and it suggests the possibility of divided ranks within the executive branch,” said Steve Aftergood, director of the project on government secrecy at the Federation of American Scientists. “Their concerns are potentially valid and they need to be taken into account, but they cannot be decisive. There are larger questions of accountability at stake that need to be addressed.”

Concerns about revealing black sites in foreign countries and cooperation with foreign intelligence agencies could be dealt with during the redaction process, he said. Some believe that even with redaction, sharp observers might be able to figure it out. Rubio and Risch’s disclosure of the State Department concerns may be part of the effort to shape the debate over what is and is not declassified.

“At this point there is a lot of signals sending going on,” said Aftergood. “There will be some declassification. So it’s a question of what get released and what gets withheld.”

In the end, there will always be some Republican opposition to declassifying a report that the Republican committee staff refused to participate in and that many in the GOP see as an effort to rehash the missteps of the Bush administration in the run up to the 2014 midterm elections. Meanwhile, the White House has to balance its desire to satisfy Congress with its need to preserve the confidence of U.S. intelligence agencies.

For declassification advocates, the momentum towards more public awareness about the CIA programs is picking up steam.

“Something wrong was done by the CIA and it’s time to say we made a mistake and make sure it never happens again,” Aftergood said.