apt-get update not working as azure custom script extension

I'm deploying linux ubuntu 16.04 LTS VMSS using Azure ARM template with custom script extension. Content of customscript.sh:

apt-get updateapt-get install build-essential -y...

but it fails at this update step itself with error:

Splitting up /var/lib/apt/lists/archive.ubuntu.com_ubuntu_dists_xenial_InRelease into data and signature failedE: GPG error: http://archive.ubuntu.com/ubuntu xenial InRelease: Clearsigned file isn't valid, got 'NODATA' (does the network require authentication?)

When I login to the VM and perform apt-get update, it runs successfully.

ARM Template for deployment of Linux VMSS using Custom Script Extension:

"virtualMachineProfile": {"extensionProfile": {"extensions": [                            {"name": "Custom Deployment","properties": {"publisher": "Microsoft.Azure.Extensions","typeHandlerVersion": "2.1","autoUpgradeMinorVersion": true,"protectedSettings": {"commandToExecute": "[concat('/bin/bash customscript.sh')]","fileUris": ["[parameters('scriptToExecuteLinux')]"                    ]                  },"type": "CustomScript"                }              },            }         ......       }

Please let me know if I'm performing any step incorrectly.Thanks in advance.