Top Cybersecurity Risks Confronting PKI Systems Today, and How to Protect Against Them

Public Key Infrastructure (PKI) is the unseen backbone of digital trust, underpinning everything from HTTPS-secured websites and VPN access to digitally signed contracts and encrypted email. Yet as organizations increasingly rely on certificate-based authentication, attackers are targeting PKI as a high-value attack surface. A misstep in your PKI security can lead to undetectable man-in-the-middle (MITM) attacks, impersonated identities, and a total collapse of your trust chain—often with catastrophic operational, financial, and reputational consequences.

Below, we dive into the top cybersecurity risks facing PKI systems today and detail best practices to safeguard your infrastructure, ensure certificate lifecycle management, and future-proof your digital trust.

1. Inadequate Private Key Protection

Risk: If a private key is exfiltrated, an attacker can impersonate your servers, issue fraudulent certificates, or decrypt sensitive data.
Indicators of Exposure:

• Private keys stored on general-purpose file servers or developer laptops

• Absence of Hardware Security Modules (HSMs) or secure enclaves

Mitigation Strategies:

• Store all root and subordinate CA private keys within certified HSMs (FIPS 140-2 Level 3 or higher).

• Enforce key exportability-disabled policies so keys never leave the secure boundary.

• Implement strict access controls with multi-factor authentication and dual-control policies for any key usage.

2. Use of Weak or Obsolete Cryptographic Algorithms

Risk: Algorithms like RSA-1024 or SHA-1 are no longer collision-resistant or brute-force safe, opening the door to cryptanalytic attacks.
Indicators of Obsolescence:

• Active certificates signed with deprecated hash functions (SHA-1)

• Templates still permitting RSA key lengths under 2048 bits

Mitigation Strategies:

• Enforce crypto-agility by phasing out RSA-1024 and SHA-1 entirely.

• Adopt ECC (Elliptic-Curve Cryptography) with P-256/P-384 curves or RSA-2048+ and SHA-256/SHA-3 for hashing.

• Maintain an algorithm upgrade policy, ensuring all new certificates comply with current best practices.

3. Mismanagement of Certificate Lifecycles

Risk: Expired or unrevokeable certificates break trust chains and can cause service outages or leave expired credentials in circulation.
Indicators of Poor Lifecycle Management:

• Mixed manual and automated renewal processes leading to gaps

• Absence of a centralized inventory of all SSL/TLS, code-signing, and S/MIME certificates

Mitigation Strategies:

• Deploy a Certificate Lifecycle Management platform that automates issuance, renewal, and revocation via policy-driven workflows.

• Maintain a single source of truth for all certificates and keys, with real-time dashboards tracking expiry dates and revocation status.

• Implement short-lived certificates (e.g., 90-day SSL/TLS certificates) to reduce blast radius in case of compromise.

4. Compromise or Misconfiguration of Certificate Authorities

Risk: A breached or misconfigured CA can issue fraudulent certificates trusted by all clients and browsers.
Indicators of CA Vulnerability:

• Root CA servers connected to production networks

• Subordinate CAs without strict issuance policies or out-of-band approval

Mitigation Strategies:

• Keep Root CAs offline (air-gapped) and use online Subordinate CAs with tight policy controls.

• Implement Certificate Transparency monitoring to detect unexpected certificate issuance.

• Perform regular CA configuration audits, ensuring policy OIDs, allowed usages, and key sizes are enforced.

5. Insecure Certificate Enrollment Processes

Risk: Weak enrollment allows attackers to request certificates under spoofed identities, enabling phishing, MITM, or code-signing attacks.
Indicators of Enrollment Weakness:

• Email-based or self-service enrollment without out-of-band identity proofing

• Hard-coded enrollment credentials in scripts or Docker images

Mitigation Strategies:

• Leverage strong identity verification (e.g., integration with enterprise IAM, smartcards, or PKI-based hardware tokens) before issuing any certificate.

• Use SCEP or EST protocols over mutually authenticated TLS for device enrollment, requiring machine credentials.

• Enforce policy-based templates that restrict certificate usages and validity periods.

6. Failure to Enforce Real-Time Revocation Checking

Risk: If clients fail to check revocation status via OCSP (Online Certificate Status Protocol) or CRL (Certificate Revocation Lists), they may accept compromised or revoked certificates.
Indicators of Lax Revocation Handling:

• Endpoints configured to “soft-fail” OCSP lookups

• CRL updates published infrequently or not at all

Mitigation Strategies:

• Configure all TLS endpoints and applications to perform OCSP stapling and enforce hard-fail on revocation lookup failures.

• Publish CRLs at short intervals (e.g., hourly) or use OCSP responders with high-availability clustering.

• Monitor revocation service health and response times as part of your PKI SLA metrics.

7. Human Error & Policy Misconfigurations

Risk: Misconfigured certificate templates, overly permissive issuance rights, or manual CA operations can inject systemic vulnerabilities.
Indicators of Misconfiguration:

• Certificate Practice Statements (CPS) that aren’t enforced in the CA software

• Administrators with “superuser” access lacking separation of duties

Mitigation Strategies:

• Develop and enforce detailed Certificate Policies (CPs) and CPS documents, mapping policy OIDs to CA configurations.

• Conduct regular PKI health checks and internal audits—automated where possible—to detect configuration drift.

• Segregate duties among enrollment officers, CA administrators, and auditors, leveraging dual-control for critical operations.

8. Shadow IT & Unmanaged Certificate Deployments

Risk: Departments issuing certificates outside central PKI governance create blind spots leading to rogue or expired certificates in production.
Indicators of Shadow Deployments:

• Unknown certificates discovered during malware scans or network audits

• Applications using self-signed certificates or outdated CA trust anchors

Mitigation Strategies:

• Utilize certificate discovery tools to scan networks, load balancers, and code repositories for unmanaged certificates.

• Enforce a policy-based block on untrusted CAs within browsers and operating systems.

• Mandate all certificate issuance go through the centralized PKI portal, with automatic enforcement in middleware and container orchestration platforms.

9. Cloud & Multi-Tenant Exposure

Risk: Deploying PKI in shared or multi-tenant cloud environments without proper isolation can allow lateral attacks across workloads.
Indicators of Cloud Risk:

• Root CA hosted in a public cloud VM without HSM-backed key protection

• Subordinate CAs sharing tenancy with untrusted applications

Mitigation Strategies:

• Choose cloud-native PKI offerings that integrate with cloud HSM services (e.g., AWS CloudHSM, Azure Dedicated HSM) and enforce tenant isolation.

• Architect your PKI on a Zero Trust model: every CA operation and certificate usage requires authentication and authorization checks.

• Regularly rotate keys and refresh credentials in cloud KMS to limit exposure in the event of a breach.

Best Practices for a Future-Ready PKI Strategy

1. Centralize & Automate

Consolidate all CAs, certificate issuance, and key management under a unified Certificate Lifecycle Management platform.

2. Enforce Zero Trust

Every PKI action—enrollment, issuance, revocation—must be authenticated via your enterprise IAM and logged for audit.

3. Adopt Short-Lived Certificates

Minimize attack window by issuing certificates with validity spans of 90 days or less.

4. Implement Continuous Monitoring

Integrate PKI telemetry into your SIEM to alert on unusual certificate issuance or revocation patterns.

5. Train & Certify Your PKI Team

Regularly train administrators on RFC standards (RFC 5280), HSM operations, and incident response for PKI compromises.

Conclusion & Call to Action

Your PKI security is only as strong as its weakest link—whether that’s an unsecured private key, an obsolete algorithm, or a shadow IT certificate. At eMudhra, our enterprise-grade solutions—emCA, emAS, and emSign—provide end-to-end certificate lifecycle management, HSM-backed private key protection, and real-time revocation services to defend against today’s most sophisticated PKI threats.