Thomas L. Hungerford, a seven-year veteran analyst with the fiercely nonpartisan Congressional Research Service, has written countless reports for members of Congress about the economic effects of various tax policy proposals.

He works pretty much as his 500 analyst colleagues at the CRS do, churning out studies and updates that seek to give members an intellectual and informational framework for the policy decisions they debate in the House and Senate.

Though treasured by members, staff and all manner of policy experts in and around Capitol Hill, the work product of Congress’ in-house “think tank” isn’t always a dry, just-the-facts-ma’am recitation of academic literature. CRS analysts can and will step out of the shadows and deliver conclusions based on their considerable expertise and research.

The problem for Hungerford and his fellow analysts comes when those conclusions inflame, rather than just inform, the debate. What’s more, the institutional policies that the CRS employs to protect its staff analysts from controversy aren’t always clear or helpful.

That complicates the agency’s relationship with Congress, which has come to expect certain results from its requests for reports.

“No one asks for anything from CRS without knowing what the answer is,” said Ike Brannon of the American Action Forum. He was previously the chief economist for the House Energy and Commerce Committee and the principal economic adviser for Senate Finance ranking member Orrin G. Hatch, R-Utah.

Hungerford, in his most recent report, wanted to answer a single question that he knew would continue to divide Democrats and Republicans as the fiscal cliff comes nearer: Was there an association between top tax rates and economic growth?

He found no association, a conclusion that went against conservative economic theory and bolstered the mainstream Democratic position.

That conclusion didn’t go unnoticed when his report was published in September. Congressional Republicans called foul on the findings, which they said were biased and methodologically flawed. When the CRS removed the report from its internal website in mid-October, Democrats accused the agency of caving to political pressure and Republicans of censoring results they did not like.

The episode made national news, but it’s just the most recent example of how the agency’s guidelines for analysts — or lack thereof — can lead to confusion, partisan tensions and, perhaps most damning, doubts about objectivity.

The controversy also reveals larger internal issues at the agency that have left not just Hungerford but others before him vulnerable to scrutiny.

The uncertainty goes back to the 1995 rise of Speaker Newt Gingrich, R-Ga., who pledged to slash spending on congressional research agencies and eliminate one such agency entirely: the Office of Technology Assessment.

Fearing a similar demise and the loss of valuable resources, management decided to “take a step back,” according to former CRS attorney Daniel Schuman.

Schuman said CRS analysts were counseled to avoid coming to firm conclusions and serve more as an aggregator of existing research.

“Realizing the danger of engaging in pure analysis, [management] tried to push everyone to not just be even-handed but to engage more in a survey of what people think as opposed to an analysis of what the options are,” said Schuman, now policy counsel at the Sunlight Foundation.

The anxiety over how to serve lawmakers without alienating them resurfaced in 2004, when former CRS analyst Louis Fisher wrote an article for an outside publication that took a personal stance on the Iraq War.

“We must all see to it that our ability to serve Congress … is not compromised by even the appearance that we have our own agenda,” then-CRS Director Daniel Mulhollan said in a response, warning that analysts “might be seen as so set in their personal views that they are no longer to be trusted to provide objective research and analysis.”

Fisher fired back: “If the front office puts emphasis on neutrality, balance and even-handedness, there is little room for careful, expert analysis.”

An analyst’s personal politics might also undermine his work on a controversial topic. In Hungerford’s case, it doesn’t help that he served in the Office of Management and Budget and the Social Security Administration in the final years of Bill Clinton’s presidency and that he has contributed more than $7,000 to Democratic campaigns since 2008.

The CRS doesn’t have a policy that requires analysts to disclose campaign contributions or party affiliations or that forbids them from pursuing outside writing and speaking opportunities as long as they make it clear they don’t speak for the agency.

Which is also a fine line: Morris Davis, a former Guantánamo Bay, Cuba, military commissions prosecutor, was fired from the CRS in 2009 after penning a Wall Street Journal opinion piece critical of the Obama administration’s policy on detainees.

Hungerford in an interview with Roll Call said he wouldn’t comment on the specifics of his case or the general state of the CRS, saying for the record only that he intended to remain at the agency where he enjoys his job and respects his colleagues.

Other analysts interviewed defended Hungerford and his report. They added that individual political beliefs have no bearing on analysts’ nonpartisan professionalism, and a strict review process is in place to guard against any breaches in that professionalism.

Hungerford was not able to separate his personal views from his professional work, according to Hatch spokeswoman Antonia Ferrier.

“In [Washington] … people have perspectives on politics, parties and candidates. That’s par for the course,” said Ferrier, whose boss is one of Hungerford’s main critics. “That’s why it is even more important and absolutely essential that CRS maintain the strictest standards in terms of analysis so they can stay above reproach.”

No one interviewed for this story suggested they had a problem with the political activity policy, or lack thereof. Everyone had different ideas on how to avoid future controversies.

Schuman said all CRS reports should be made public rather than published first on a Congress-only website. A senior GOP aide suggested the current review system for the CRS needs to emulate that of the Congressional Budget Office, an “independent, transparent peer-review process involving input from outsiders.”

CRS spokeswoman Janine D’Addario suggested in a statement that the agency was very much aware of the issues at stake.

“CRS’ mission is to ensure Congress has available the best possible research and analysis on which to base its decisions and that it is aware of the options and consequences that may surround a particular issue,” she said. “Our action in temporarily withdrawing the report was motivated by this and not the result of political pressure.”

An earlier version of this article incorrectly characterized former CRS analyst Louis Fisher’s position on the Iraq War as partisan. He did not side with Democrats or Republicans.