The chief watchdog overseeing the Environmental Protection Agency is accusing agency officials of obstructing investigations by refusing to cooperate, using bully tactics to silence lower-level workers and, in at least one instance, threatening an agent.

EPA Inspector General Arthur Elkins Jr. made the allegations in a letter sent this week to Sen. David Vitter, R-La. The senator earlier had questioned both the objectivity of the IG office and whether EPA officials had interfered with investigations -- specifically asking about the case of John Beale, a former high-ranking official who was sentenced in December to 32 months in prison for bilking taxpayers of nearly $1 million by pretending to be a CIA agent.

The IG's office formally exposed the Beale fraud last year, but revealed to Vitter that, in this and other cases, its agents ran into resistance and even "intimidation" from the EPA ranks.

"Over the past 12 months, there have been several EPA officials who have taken action to prevent [the Office of Investigations] from conducting investigations or have attempted to obstruct investigations through intimidation," Elkins wrote.

In the Beale probe, Elkins confirmed that a staff attorney refused to be interviewed on a related audit following Beale's prosecution. Elkins wrote that auditors found indications she may have been aware of concerns about Beale's pay months earlier than she let on.

More On This... Supreme Court appears divided in battle over EPA climate regs

Separately, Elkins said an official in the agency's Office of Homeland Security approached one of their agents "in a threatening manner" during an investigation, preventing the agent from doing her job. The same official allegedly "issued non-disclosure agreements to EPA employees that prevented these employees from cooperating."

The case was apparently reported to the Justice Department, but it was never prosecuted, according to the letter.

Elkins said that yet another employee in the same office also refused to cooperate in an IG probe, and pulled the same move -- issuing non-disclosure agreements to employees to prevent them from cooperating as well.

In response to the letter, EPA Deputy Administrator Bob Perciasepe claimed the incidents were "isolated events" and involve a "fraction of a percent of the EPA's 16,000 employees." Perciasepe wrote to Elkins on Thursday saying the IG's letter "omitted important context" -- in the response letter, obtained by FoxNews.com, Perciasepe explained that most of the incidents reflected a "difficult disagreement" over the EPA's role in investigating national security matters. He suggested the EPA does not agree with the IG's office that it has authority to investigate those issues.

In the letter, he voiced concern that some in Congress and the media were drawing "unfair conclusions."

Earlier, Vitter pointed to the IG's claims as proof of deeper problems at the agency.

"We are starting to see proof of what we had already suspected -- John Beale's time and attendance fraud was the tip of the iceberg at the EPA," Vitter said in a statement. "The whole agency seems to be in complete disarray, which is exactly why we need to have a full [Environment and Public Works] Committee hearing on the fraud surrounding this case and other prevalent problems."

Vitter is the top Republican on that committee, which has been digging into how Beale was allowed to get away with his deception for so many years. Previously released documents have shown that some agency employees had suspicions about Beale for a long time, yet he kept receiving improper bonuses until 2013. Those bonuses totaled about $500,000.

Vitter had also raised concerns about the IG office's independence. But Elkins defended its work and its findings. He stood by a claim that EPA Administrator Gina McCarthy was the first senior official to report Beale. And he refuted claims that it viewed Beale's supposed CIA status as a human resources issue. The letter noted that other agency officials discussed the controversy in that context, but said "OIG was not part of these discussions."