Check to see if your VM's cpu has any additional features enabled like VT (virtualization technology), as well as if the machine is running in BIOS or EFI mode (In virtualbox these are all listed in under CPU, however in VMware player only some are listed the rest can only be configured by editing the vm config file manually in notepad. The best option is to have all such things turned OFF unless you really need them, which is the default setting of most VM softwares.
Check to make sure you choose the correct VM type, for example in VMware Player you would choose Ubuntu 64 rather than Ubuntu when deciding what type of VM profile to use.
If the issues persist, try uninstalling the VM software and re-installing (or if possible updating to a new release).
Last but not least check you HOST bios or uefi, MANY VM PROGRAMS REQUIRE VT or VT-x etc to be enabled on the host to run 64bit vms.