A new federal executive order aimed at eliminating fraud, waste, and abuse signals a clear shift for healthcare and not-for-profit organizations that receive federal funds. While oversight of federal programs is nothing new, this order formalizes a cross-agency task force and raises expectations around documentation, internal controls, and accountability, particularly for organizations that participate in Medicaid, Medicare, and federal grant and assistance programs.
The message is straightforward: organizations that rely on federal dollars should expect closer scrutiny and should act now to strengthen their compliance posture.
What the new federal executive order means for healthcare and nonprofit organizations
The executive order establishes a task force charged with identifying and reducing fraud, waste, and abuse across all federal benefit, assistance, and grant programs. Importantly, it applies broadly across federal agencies and explicitly includes:
- Federal grants
- Federal assistance programs
- Programs administered directly by federal agencies
- Programs jointly administered with states, such as Medicaid
This means the implications extend well beyond traditional healthcare billing audits. Federally Qualified Health Centers (FQHCs), hospitals, clinics, and not-for-profit organizations that participate in programs such as Head Start, WIC, housing assistance, and other federal grants are all within scope.
Why increased federal oversight matters for federally funded programs now
Federal administrations have long emphasized fraud prevention, but this executive order elevates coordination and enforcement.
Organizations should expect:
- Increased audit activity and agency oversight
- More restrictive language in grant agreements and program participation terms
- Heightened focus on eligibility verification and allowable use of funds
- Greater scrutiny of internal controls and documentation practices
In short, regulators are looking not just at whether policies exist, but whether organizations can prove through documentation that controls are working in practice.
Why documentation and compliance evidence are critical under federal grant oversight
A recurring theme of the executive order is documentation. Policies alone are not enough. Organizations must be able to demonstrate that their controls are consistently followed and supported by evidence.
Key documentation expectations include:
- Evidence of review and approval for grant drawdowns and funding requests
- Documentation supporting patient or beneficiary eligibility
- Proof that expenses charged to grants are allowable and appropriate
- Clinical documentation that supports Medicare and Medicaid billing
For healthcare providers, this reinforces a familiar principle: if it is not documented, it did not happen. The same standard increasingly applies across grant and assistance programs.
Internal controls requirements for federal grants and healthcare programs
The executive order effectively raises the bar on internal controls. While written policies remain important, regulators are focused on whether organizations are applying those controls consistently and correctly.
Strong internal control environments include:
- Clear segregation of duties
- Defined review and approval processes
- Documented evidence of oversight
- Ongoing monitoring and periodic reassessment
For example, if an organization’s policy states that grant drawdowns require supervisory approval, there should be clear documentation showing who reviewed and approved each request.
Controls must be embedded in daily operations, not treated as paperwork exercises.
Subrecipient monitoring risks for federal grants and assistance programs
Organizations that pass federal funds to subrecipients face additional exposure under the executive order. If you receive a grant and distribute funds to partner organizations to meet program objectives, you retain responsibility for compliance.
That includes ensuring subrecipients:
- Follow comparable internal controls
- Maintain adequate documentation
- Meet eligibility and allowability requirements
In practice, this means organizations must actively monitor subrecipients instead of assuming compliance. Weak controls or documentation at the subrecipient level can still result in findings for the primary grant recipient.
Penalties and risks of noncompliance with federal grant and program requirements
The risks associated with inadequate documentation and controls are significant. Depending on the severity of findings, organizations may face:
- Repayment of federal funds
- Financial penalties or damages
- Loss of program eligibility
- Termination from federal programs or grants
In many cases, organizations act as intermediaries, passing federal dollars to beneficiaries. If eligibility documentation is insufficient, the organization, not the beneficiary, bears responsibility for repayment and penalties.
Beyond financial impact, losing eligibility to participate in a major federal program can threaten an organization’s long-term sustainability.
How healthcare and nonprofit organizations should prepare for increased audits
This executive order does not introduce entirely new requirements. It reinforces what organizations should already be doing. However, it creates urgency.
Now is the time to:
- Review and update policies and procedures
- Assess whether controls are implemented consistently in practice
- Identify gaps caused by staff turnover or process changes
- Strengthen documentation standards across programs
- Revisit subrecipient monitoring processes
For many organizations, this is an opportunity to “kick the tires” on compliance programs and make sure documentation aligns with how work actually gets done.
Preparing for increased federal audits, enforcement, and oversight
The federal government is signaling that more oversight is coming. Organizations should expect tighter controls, increased reviews, and less tolerance for undocumented processes.
Preparing now by reinforcing internal controls and documentation can help organizations reduce risk, protect critical funding streams, and demonstrate compliance when auditors come knocking.
The takeaway is clear: it is time to dot the i’s, cross the t’s, and make sure every federal dollar received is fully supported.
Key takeaways
- Federal oversight is increasing. A new executive order establishes a cross-agency task force focused on fraud, waste, and abuse across federal grants, assistance programs, and jointly administered state programs.
- Healthcare and not-for-profits are squarely in scope. Organizations participating in Medicare, Medicaid, FQHC programs, and federal grants or assistance programs should expect heightened scrutiny.
- Documentation matters more than ever. Policies alone are not enough. Organizations must be able to show documented evidence that controls are consistently followed in practice.
- Internal controls must be operational—not theoretical. Review, approval, eligibility verification, and monitoring processes must be embedded in day-to-day operations and supported with clear audit trails.
- Subrecipient compliance is your responsibility. Grant recipients remain accountable for ensuring subrecipients maintain adequate controls and documentation.
- The financial risk is real. Noncompliance can result in repayment of funds, penalties, loss of program eligibility, and the disruption of critical revenue streams.
- Now is the time to act. Organizations should review and update policies, assess control effectiveness, and address gaps before increased enforcement activity begins.
About BerryDunn
BerryDunn is a full-service assurance, tax, and advisory firm serving healthcare organizations and nonprofits nationwide. We work with hospitals, health systems, federally qualified health centers (FQHCs), and mission-driven organizations to navigate complex regulatory, financial, and operational environments.
Our teams bring deep experience in healthcare and nonprofit audits, compliance, and governance, along with specialized grant consulting services that help organizations strengthen internal controls, manage federal funding responsibly, and remain audit-ready. Through a practical, collaborative approach, BerryDunn helps organizations protect critical funding streams and sustain their mission.