vCenter virtual machine NTP synchronization fails with "Clock Unsynchronized" error

Products

• VMware vCenter Server

Issue/Introduction

• The vCenter Server Appliance (VCSA) fails to synchronize time with configured NTP servers, resulting in a persistent time offset
  
  
• Running ntpq -p shows reachable remote servers, but with a high offset (e.g., > 100,000 ms):
  

       remote           refid      st t when poll reach   delay   offset  jitter
  ==============================================================================
  NTP-1         1 u   60   64   17    7.158  +108007 62357.4
  NTP-2          1 u   53   64   17    2.692  +108006 62357.4

   

• The following error is observed in journalctl -u ntpd -n 1000:
  <timestamp> <vCenter FQDN> ntpd[12968]: kernel reports TIME_ERROR: 0x2041: Clock Unsynchronized
  
  
• Manual attempts to force a time sync using ntpdate may fail or, if successful, the clock immediately reverts to the incorrect time.

Cause

The issue is caused by a conflict between the VCSA guest operating system's NTP configuration and the VMware Tools time synchronization setting. When "Synchronize guest time with host" is enabled, the ESXi host's clock acts as an external override. If the ESXi host time differs from the NTP source, the VCSA clock will repeatedly revert to the host time, preventing NTP from maintaining a stable lock.

Resolution

To resolve this issue, you must disable the VMware Tools time synchronization to allow NTP to be the sole authoritative time source.

Disable Host Time Synchronization (vSphere Client)

1. Log in to the vSphere Client.
2. Locate and select the VCSA Virtual Machine in the inventory.
3. Select Actions > Edit Settings.
4. Navigate to the VM Options tab.
5. Expand the VMware Tools section.
6. Under Time, uncheck the box for Synchronize guest time with host.
7. Click OK.