For posterity, I'll provide a workaround for others.

1. Uninstall flatpak from the default repos first, because the PPA will
not upgrade the version provided from the Ubuntu Universe repo.

```
sudo apt remove flatpak
```

2. Install flatpak from the Flatpak PPA:
https://launchpad.net/~flatpak/+archive/ubuntu/stable

```
sudo add-apt-repository ppa:flatpak/stable
sudo apt update
sudo apt install flatpak
```

And check:

```
% flatpak --version
Flatpak 1.18.1
```

-- 
You received this bug notification because you are a member of Ubuntu
Bugs, which is subscribed to Ubuntu.
https://bugs.launchpad.net/bugs/2163587

Title:
  Flatpak package in Universe is 2 years old & is missing critical
  security updates

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https://bugs.launchpad.net/ubuntu/+source/flatpak/+bug/2163587/+subscriptions


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