Some dental clinics start out running payroll manually. A spreadsheet here, an email approval there, maybe a calendar reminder for remittances. It works, until it doesn’t.
Manual payroll often isn’t a conscious decision. It’s a system that grows organically, shaped by urgency and good intentions. The problem is that as a clinic grows, even slightly, that system becomes fragile. And when it breaks, the consequences tend to show up in the form of CRA penalties, interest, and stressful audits.
Here are the most common and most overlooked CRA risks that come with manual payroll.
Manual payroll increases the likelihood of minor inconsistencies, such as rounding differences, incorrect CPP or EI calculations, or mismatched totals between payroll runs and reported amounts.
Individually, these errors can feel insignificant. From the CRA’s perspective, they’re signals.
The CRA doesn’t assess payroll based on intent or effort. It assesses outcomes. If deductions are calculated incorrectly or reported inconsistently, even by small amounts, the clinic is still responsible for correcting them, often retroactively, with interest.
Over time, a pattern of small discrepancies can draw scrutiny and increase the likelihood of a deeper review.
One of the most common compliance issues the CRA sees is late remittances.
When payroll is managed manually, remittance schedules are often tracked in someone’s head, inbox, or personal calendar. All it takes is a vacation, a busy month, or a role change for a deadline to slip.
Late remittances trigger penalties quickly. Repeated delays increase penalty rates, and interest accrues from the original due date, even if the amounts owed are small.
What makes this especially painful is that many clinics did withhold the correct amounts from employees. The issue isn’t payroll accuracy. It’s timing. And timing matters to the CRA.
The CRA expects employers to maintain clear, consistent payroll records. That includes how pay was calculated, when changes were made, who approved them, and what was reported and when.
Manual payroll often relies on scattered documentation. Spreadsheets saved under different names, email chains for approvals, and informal change tracking are common. During a CRA review, reconstructing this history can be difficult or impossible.
Gaps in records don’t just slow down audits. They can shift the burden of proof onto the clinic.
Manual payroll systems tend to be person-dependent. One team member knows how the spreadsheet works. One person remembers the edge cases.
When that person is away, or leaves, the system becomes vulnerable. Knowledge gaps lead to errors, and errors lead to compliance risk.
This is especially relevant for clinics with variable staffing, temporary coverage, or frequent onboarding. The more dynamic the workforce, the harder it is to safely manage payroll by hand.
Manual payroll can feel good enough in the early days. But compliance risk compounds quietly.
More team members, more pay periods, more changes, and more reporting obligations all increase the chance of something slipping through the cracks. By the time a problem surfaces, it’s often been building for months or years.
Reducing CRA risk isn’t about eliminating human involvement. It’s about reducing reliance on memory, manual calculations, and fragmented records.
Modern payroll systems help by automating calculations, standardizing remittance schedules, and creating consistent, timestamped records. When approvals, changes, and reporting live in one place, compliance becomes easier to maintain and far easier to demonstrate if questions ever arise.
This matters even more for dental clinics managing both permanent staff and temporary team members. Running payroll through multiple systems, or mixing manual processes with software, increases complexity and risk.
Fairly Payroll for Temps and Teams was built to solve this exact problem. By unifying payroll for permanent staff and temps in a single system, clinics benefit from consistent CRA-compliant calculations, clear audit trails across all workers, and centralized records for pay, changes, and approvals. Fewer handoffs mean fewer gaps.
Manual payroll rarely fails all at once. It fails quietly, through small cracks that widen over time. A unified payroll approach helps close those cracks early, protecting both your clinic and your peace of mind.