Using Let's Encrypt for an internal website is not inherently insecure. However, using a publicly trusted CA for an internal-only application has some considerations:
1. Certificate Transparency: Publicly trusted certificates are logged in Certificate Transparency systems. Internal hostnames such as vpn.company.com or payroll.company.com may therefore become publicly discoverable.
2. External dependencies: DNS-01 certificate issuance and renewal can depend on your DNS provider, DNS API and Internet connectivity.
3. DNS credentials: Automated DNS-01 requires access to DNS infrastructure. Those credentials need to be carefully protected and restricted.
4. Public trust: An internal HRMS or ERP normally needs to be trusted only by authorized company devices. Public CA trust may therefore provide more trust than the application actually requires.
These are architectural considerations, not vulnerabilities in Let's Encrypt itself.
A Private CA provides an alternative in which the organization controls certificate issuance and which devices trust the CA.
In short: The question is not whether Let's Encrypt is secure, but whether public Web PKI is the right trust model for your internal applications.
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