President Trump is under many microscopes right now.

Not only did he allude through a tweet on Friday that he is the subject of an internal investigation by special counsel, but on the same day, an independent federal agency commissioned under Congress also said “grave concerns” were prompting an investigation into federal civil rights enforcement within his administration.

The United States Commission on Civil Rights, a bipartisan agency charged with advising the president and Congress on civil rights matters, unanimously approved a comprehensive two-year probe into the “degree to which current budgets and staffing levels allow civil rights offices to perform” their functions within the administration, said the agency in a statement.

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The federal watchdog group became concerned about the Trump administration after several agencies announced budget and personnel cuts in departments that oversee civil rights. The "proposed cuts would result in a dangerous reduction of civil rights enforcement across the country, leaving communities of color, LGBT people, older people, people with disabilities, and other marginalized groups exposed to greater risk of discrimination," said the statement.

The commission, created under the Civil Rights Act and funded by Congress, expressed specific worry in seven agencies under the president, including the Department of Education and the Department of Justice.

The “repeated refusal” of Education Secretary Betsy DeVos to commit to enforcing federal civil rights during Congressional testimony coupled with deep budget cuts within the agency’s Office of Civil Rights is “particularly troubling,” the agency added in the statement.

DeVos was asked during a Senate subcommittee hearing earlier this month whether discrimination against LGBTQ students in private school would be allowed.

Education Secretary Betsy DeVos testifies on Capitol Hill in Washington, Tuesday, June 6, 2017. Susan Walsh / AP file

While she did say “schools that receive federal funds must follow federal law,” she did not commit to banning discrimination, saying that area of law is “unsettled.”

The Department of Education did not return a request for comment by NBC News.

The commission also wants to look into the Department of Justice, which it says has completely changed its priorities.

“Actions by the Department indicate it is minimizing its civil rights efforts,” the statement said. “For example, a majority of the Commission criticized DOJ’s decision to site Immigrations and Customs Enforcement officers in courthouses as a dangerous impediment to access to justice for all Americans,” the statement said.

The investigation will also look into the departments of Labor, Housing and Urban Development, Health and Human Services, Environmental Protection Agency and the Legal Services Corporation — which are all expected to slash budget and personnel that monitor civil rights.

While the commission does not have the ability to enforce the findings of its investigation, it will present the final report to Congress at the end of 2019. After that, it’s up to legislators to act.

“For 60 years, Congress has charged the Commission to monitor Federal civil rights enforcement and recommend necessary change,” said Catherine E. Lhamon, who chairs the Commission. “We take this charge seriously, and we look forward to reporting our findings to Congress, the President, and the American people.”