I am trying to delete a file using a custom action scheduled between InstallInitialise and InstallFinalize standard action.
MajorUpgrade element is used to design upgrades.
However, I want the custom action to run only during uninstall and not during the Major upgrade(this includes uninstall and install).
I have used the following conditions to execute the CUstom action:
(NOT UPGRADINGPRODUCTCODE) AND (REMOVE="ALL")REMOVE AND NOT WIX_UPGRADE_DETECTED
Is there a way to uniquely detect the Major Upgrade using properties in Wix?

It's not obvious whether you want to do this in the older installed product (which is presumably already shipped and therefore can't be changed without an update such as a patch) or in the newer upgrade install.
I'll also assume you've looked at the RemoveFile element and it doesn't meet your requirements.
The UPGRADINGPRODUCTCODE property applies to the older product being upgraded and uninstalled. If the file belongs to that installed product and you want to remove it only at uninstall with a custom action in that older install the condition on the custom action would be:
REMOVE="ALL" and not UPGRADINGPRODUCTCODE
but as I said, that custom action would need to be already in the older installed product and there's nothing you can do in your upgrade MSI to fix that.
If you are removing the file from the upgrade then the condition during an upgrade is only:
WIX_UPGRADE_DETECTED
It might also help to say where your major upgrade is sequenced. If it's early (such as around InstallInitialize) then the upgrade is basically an uninstall of the older product followed by an install of the newer product, and that might be related to the removal of the file, if that's what you're seeing.